In TES lore, soul trapping humanoids is related to necromancy and is believed to be immoral. However, soul trapping creatures is perfectly acceptable.
According to Skyrim Wiki, this is because:
The souls of humanoids trapped in these soul gems remain conscious.
They are generally regarded as unethical, and their use is prohibited
at The College of Winterhold, despite the institution's lenient stance
on the practice of Necromancy. Soul Trapping humanoids is considered a
crime in many of Skyrim's Holds.
However, I am unable to find any justification for this from in-game sources.
Best Answer
It's not just soul trapping black souls that is considered immoral, but every aspect of necromancy, from the in game book The Black Arts On Trial (You have no idea how many times I typed Dark Arts...).
As soul trapping black souls falls under necromancy it will also corrupt the caster's soul. It's also counter to the will of Arkay and anyone knows messing with a god is a bad idea.
There are some things related to Necromancy that are acceptable, the conjuration spell such as Guardian Spirit can summon a spirit from the afterworld, but the difference is that the summoning is with consent unlike with necromancy.