Because they know how to and are capable of making sentient holograms, but don’t, means that they are willingly choosing to strip free will from holograms.

Creating puppets instead of people is not stripping free will from anything.

Janeway erases all of Sullivan’s memory of his wife and deletes her. She then coerces him via rewriting his programming to have a relationship with her.

Most holograms aren't sentient. They are little more than chat bots with greater capacity, and a physical avatar.

The issue with The Doctor is that he is, in some indefinable way "special." I like him as a character, but the trechnobabble is unacceptable.