Why would he "harm his career?" Probably because HE DOESN'T CARE about making franchise films with big corporate film studios. He'll most likely continue to create smaller, more personal projects and distribute them whichever way he feels is best. Not every director is salivating to work on a comic book film or a Star Wars movie. Not every director is ready to lay prostrate in front of some corporate studio, begging for their "big break" and doing whatever it takes to achieve it. Different strokes for different folks. As a fellow creator myself, I wish Trank the best. I admire a person who doesn't hold back and says what they feel, circumstances be damned.
Fox is a big company, they can take a couple of lumps here and there and not lose their status. When the day is done, regardless of whatever goofy rumors circulated on 4chan or who-the-f-cares-where-else, Fox is responsible for how this films does. They made the decision to hire him, they funded the project, and they had final say on the outcome of the film.
I bet in about a year from now, nobody is going to even care about this film, the silly rumors that floated around, or whether or not Josh Trank has a "career' anymore.