Peter's taking photos of Spider-Man is VERY much a morally ambiguous gray area, I'd agree, but there are key differences between him profiting off being Spider-Man's paparazzo, versus him being a paparazzo to other people:
1) If he were to be a paparazzo to other people, he'd be doing damage to their lives, but as long as he sticks to being a paparazzo of himself, then the only person he's really hurting is HIMSELF ...
2) ... And, well, okay, arguably Jonah as well, except that we're frequently shown a) how poorly Jonah has treated Peter as an employee, and b) how journalistically unethical Jonah's treatments of Peter's photos has been anyway, so if Jonah were ever to go all HOW COULD YOU COMPROMISE MY JOURNALISTIC REPUTATION BY LYING TO ME with Peter, and unlike the PAD story during Civil War, all that Peter would really have to do to shut him up would be to say YES BECAUSE YOU WERE SO COMMITTED TO THE TRUTH WHEN YOU FOUND A WAY TO PRESENT EVERY PHOTO AS EVIDENCE THAT I WAS A THREAT AND/OR MENACE.
Bottom line, though, even if you or I don't agree with Peter's morals wioth regard to his photojournalism, he DID have a moral line that he wouldn't cross ("Exploiting myself and Jonah for personal gain is okay, but exploiting others isn't"), which BND refuses to acknowledge ever existed.