I usually make the right decision when it's overdue, so in more cases than not properly set up auto-use saves my skin. When I'm down to 20% I have all set up for quick heal and survivability, in opposition to pre-auto-use just setting it up
I'm almost totally new to the game so I don't even know exactly how anti-magic interruption works, but there should be numerous ways to account for it. For example, keep in memory that certain auto-use thingy "burned" the turn and if it does so on it's two next auto-uses (unless something was changed in auto-use itself) pop-up a message. Or keep a turn-counter when automatic use is active and playing and let player decide how many of them can pass before a breaker jumps in. Best case scenario - detect that interrupable equip is set to auto-use and automatically turn off (totally) auto use for that piece when it's interruption chance gets too high, while giving you a msg of "too unreliable to risk auto-use".
I THINK I've lost a life due to that earlier, when all of a sudden everything got a lot of things going on, but at the time I thought I just got hit by some nasty debuff.