Players have been cheating death in roguelikes for as long as there have been roguelikes. Originally, this was done via "save scumming" (copying save files as backups), but there are other ways to cheat and avoid death. Consequently, cheating has long been supported as an in-game feature (if you want to cheat, then cheat, and don't pretend you're not cheating!). I have been guilty of cheating myself. I was a prolific save-scummer back when I started playing Moria. I became so adept at save scumming that I even used it to get favorable RNG outcomes, such as better loot drops. This was a long time ago, and I was young and naive. The game remained somewhat interesting while cheating, but it became less challenging, less engaging, and less fun. At times it was tedious and boring. Other former cheaters have similar tales... and the same lesson learned: roguelikes are much more fun if you don't cheat! (and infinite lives is equivalent to cheating)
Nevertheless, there is a reason we cheated in the first place. I didn't like perma-death. It didn't seem fair to me. Roguelikes can be looooong. I could play as a single character for several weeks or even several months. Why would I risk losing all that playing time if the Random Number Gods (RNG), who could kill me on a whim, decided to be spiteful and end my game? If I died on level 70, I didn't want to spend the next few weeks redoing levels 1-70 again with a new character--what a waste of time! Moria was "only" 100 levels, and if I remember correctly how it played, it was a shorter game than ToME is now. When I played it (a little bit each evening), though, it didn't seem short at all. I was young and new to roguelikes, and the full gaming experience didn't feel accessible to me unless I cheated, which was most unfortunate. If there had been a kinder playing option between perma-death and cheating--and less extreme than either perma-death or cheating--I would have happily chosen it. A "middle way" playing mode would ideally make the game more accessible while keeping it challenging, fun, and fair. Indeed, what I wanted was... Chapters!
Summary
Every zone in ToME is considered a chapter. If you die during a chapter, then you will be penalized for the rest of the chapter. There is no perma-death. However, if a character dies several times during each chapter, then the game will become exceedingly difficult, and the player should be encouraged to start a new character (or become a better player

The "Chapters" playing mode will make the game more accessible in a fair and legitimate manner for those who choose this option. It does not need to be limited to beginners either: the difficulty of the game can be tweaked to challenge even the most insane among us.
The design goals, of course, are to make this mode simple, intuitive, fair, fun, etc. In order for Chapters to "just work"(tm), several subtle changes will need to be made in this mode.
Details
Death: back from the brink
Your character reverts to a previously saved state after dying. I would save the state between each level of a zone (but one could also save at the beginning of the zone only, but this would result in more tedium of redoing the zone). When you restart a level after dying, the level would be regenerated (as in if you died in Dreadfell(5), then the generator creates a new level for Dreadfell(5)). This removes the tedium of redoing the same level and avoids possible meta-game scumming, such as if you failed to save an escort, you could purposefully die and try to save it again using your knowledge of the level.
Creating a new level also gives the player a chance to avoid what killed them before--maybe the Random Number Gods will be kinder next time (or maybe not!). In my very limited experience with playing with multiple lives, deaths seem to occur in clusters: what killed you once can often kill you several times (maybe it was an out-of-level enemy, a particularly difficult elite, or just an unfriendly mob that you couldn't avoid). If you die in a level, there is no guarantee whatsoever that you'll get the same loot or the same vaults with the new level, so if you find something you really like, don't die!
Death: penalties
Each time a character dies in a chapter, they will receive 30% less XP than before (so one death is 70% XP, two deaths 49% XP, three deaths 34.3% XP, etc) for the rest of the chapter. Additionally, each death reduces the number of random drops in a level (nb_object) by one. Penalties for one chapter do not carry over to other chapters.
Loose ends
Stair-scumming
I strongly recommend disallowing stair scumming in this mode. When you enter a new level, you can't return to the previous level until you kill all hostile npcs.
Rod of Recall
Leaving a level always creates a saved state, which also saves the level that you are leaving. Leaving via the Rod of Recall is no different. Hence, if you recall out of Dreadfell(5), then later return to Dreadfell(5), dying there won't cause a new Dreadfell(5) to be regenerated, because the level has been saved.
Also, after a player dies and a new level is generated (or not), I would have the game give a message like "You feel disoriented for a second as if waking from a bad dream, and the Rod of Recall is oddly warm...". I would also put the Rod of Recall on full cooldown, 0/400 energy.
In-game resurrections
Perhaps give the player a choice to use in-game resurrections when they die. This would avoid the death penalty and the regeneration of the level.
Special zones
Zones such as the assassin lord/lost merchant quest, farportal zones, kryl feijan crypt, dreadfell ambush, etc., should be a single attempt only. Hence, if you die, you do not receive another chance to continue with the zone.
Worldmap enemy encounters
Hum. Not sure. I'm still thinking what would make sense if a character dies in a worldmap ambush. Any ideas?
Escorts
I don't think anything needs changed. They are random upon level generation if applicable. Hence, if you die on a level with an escort quest, you may have a different escort quest with the new level. If scumming for favorable escorts (at the cost of reduced XP and loot) is a concern, then I would have subsequent regeneration of levels use the same escort type as the first level generation.
Unlocks and achievements
I don't think anything needs changed here, either. We could be sticklers and have it so you can only recieve unlocks if you haven't died in that zone (or whatever is appropriate), but that's unnecessary imho. We could still disable unlocks with the easiest difficult level (analogous to discovery mode).
Elisa, your personal scry
I would expect a little more dialogue with her in chapters mode. If you died a lot in a zone and want to recover some XP in a comparable or easier optional zone, then you should be able to ask her for guidance (i.e., Elisa: "I heard of a rebel faction near Elvala / corrupted forest near Shatur" and so on. Before you enter a zone, perhaps she could tell you what (if anything) she knows about it and if she thinks you're prepared.
Incentives, rewards, and awards
I don't know if anything would make sense here, but having chapters does make additional incentives/rewards/awards possible.
Difficulty
Different difficulty levels should be available to choose from. Instead of changing the number of lives (as was previously done), we could modify the following parameters: XP gained, level of enemies, hitpoints, % damage, % healing, and so on.
Disclaimer
I'm sure I'm missing some things I meant to write, and I know I didn't fully explain each design decision. If you have questions or concerns, then ask or share. If Chapters does make it into ToME, I can almost guarantee that it won't be exactly as I described it here.