Honestly, I don't see your problem. I admit not to knowing Enchantment any too well (when I play a specialist, it's usually the first school to go), but I've tackled A LOT the problem of playing a necromancer with good, or at least definitely non evil, alignment. And when it comes to necromancy, it's not just nuking with a different energy, it's playing with the very stuff of undeath... a lot of the offensive spells are not plain nukes, they are curses: inflicting blindness, diseases, paralysis, curses, negative levels... and of coursze, there are the undead raising ones... so, yeah, playing with all of that without going over to the dark side is a real challenge. (and usually, I have to renounce to the undead creation spells pure and simple... disrespect to the dead, any dead, is an easy step to take, but it's a real slippery slope)
As for Enchantment, true, a lot of the high profile spells are about influencing and manipulating others... the secret to using those while being good is summed in three word : intent, restraint, respect.
-Intent : using that artificial influence for good intents and purposes, using it to make the unrighteous act for good.
-Respect : respect those you influence, don't force them to do stuff too far out of character, don't put them in hot water unless absolutely necessary, do see that they can return to a more or less normal existence when they stop being your puppet... if at all possible, act toward them in such a manner that, once free of your influence, they see you as a friend, not as that crud $£§%& who messed with their mind.
-Restraint : don't make them do stuff just because you can, keep a light touch, don't mess them up for pleasure.