One idea I had that I think would solve some of your design issues is to make all the spells limited use. Healing abuse etc. would not be such a problem, plus it gives more purpose to finding more spells further down the dungeon, instead of just getting a good set of 3 and sticking with those the whole game.
Interface wise, having spell bubbles start full, with a level that gradually depletes as they are used, seems like a good idea.. A picture explains much better:

Here, the first spell has been used quite a lot, the second spell is nearly full, and the third hasn't been used at all. An "empty" bubble (such as the way spells are currently shown) should mean exactly one use left.
In any case, I hope you expand this into a full game, because it's lots of fun.