The underlying assuming here is that antimagic should be a valid option for all (non-spellcasting) classes.
I haven't heard anyone provide a reason why this should be true.
I think it comes down to anti-magic being a big part of the game's lore, and something that not only takes some effort to get, but more effort to survive having. It could work for anti-magic to be a personal burden, requiring deep resolve to maintain (i.e. a challenge mode), but the lore tends to treat anti-magic users as powerful, dangerous (bigoted) witch-hunters. That implies the other end of the gamist spectrum, which is that anti-magic should be an alternate path, but not a lesser one. At the very least, trap options are problematic because they can frustrate new players -- imagine struggling through to, say, level twenty for the first time before taking anti-magic, losing your best gear, then dying.
I think ToME generally does pretty well at having major build paths be interesting, if not equally powerful. And for a roguelike having challenge modes is both traditional and fun, at least for some of its players. I guess the question comes down to how many people are having fun with antimagic in its current state, either as a tool against the vile magic-users or a challenge mode, versus how many people don't even consider it as a real choice because it doesn't interest them.