but I couldn't really find any benefit to disabling an opponent over just eliminating them.
2 primary reasons and two minor:
Capturing enemies reduces your "submission" reputation and
does not reduce your reputation with that faction. You'll occasionally find NPCs from "neutral" factions randomly deciding they want to attack you. Outright eliminating them is a real good way to turn the whole faction hostile whereas binding and then capturing them does not have the same effect.
One more minor reason is that there's certain pieces of armor/bindings you can obtain from goddess quests which recharge your mana pool whenever you capture enemies. Though you alluded to how this quickly becomes irrelevant as there is now passive mana pool regeneration. Another is that there's spells which can turn helpless enemies friendly and/or useful. "Conjure display stand," for example, restores 50 weapon charge for every defeated NPC you use it on at the cost of 10 mana while also turning them into convenient punching bags for other enemies.
I'll be honest. Every run I do is as the "trainee" class for fetish reasons. The two builds I've had the best success with:
-Slime
Starts out weak, but there's a ridiculous power spike once you can summon slimes as allies. They can do all the work for you so long as you've got mana to burn (note this was ridiculously broken even before renewable mana was introduced).
[Edit: it's definitely worth a mention that these slimes
do not count towards your "max summons" cap. You can swarm the whole map with these things to clear dungeons with ease.]
-Metal
It's simply good tempo. "Conjure cuffs" into "Conjure chains" is a very solid combo that stays relevant even deep into a new game+. It's also where you get the "Conjure display stand" spell I mentioned earlier. I personally don't make much use of this, but metal also has the "Steel rain" spell which adds a toy to any enemy with any level of bondage. You can combine this with "CMD: vibrate" if you want to have a little fun.
I hope this little rant has given you some ideas for future runs.