According to the lore, it is a extremely evil act to use Soul trap on a Human/Mer/Beast race (anythings that fit on black soul).
Btw, when you recharge a weapon the soul is released, so you are freeing it.
Since you are dead when inside a soul gem, you can't feel anythings, so it should not be that bad (in my point of view).
Soul trapping captures the energy. The soul is recycled.
I don't think so, in one of the TES, a quest involve looking for someone inside a soulstone, and he is well conscious, so he is inside, it is not some lifeless energy that is stored inside, it is a real form of existence.