No matter which way you look at it, as a creator, you're always going to come up against what your vision is and what you want your sales to be when you have a book you know will be at least somewhat controversial.
Creating comics is an expensive proposition. Most of us don't have money we can just throw away, but as creators, we also have a burning desire to get the things we have in our imaginations out into the world, no matter what the subject may be.
This is where the conflict arises, because what we want is to have our vision undiluted and widely disseminated. This means we're in the eyes of the buying public. Depending on what it is we want to create, we may need to either tone it down or keep it to ourselves—or go very underground with it. Underground, however, doesn't make for wide dissemination.
When you have to make a choice, what do you do?
No one can answer this question for you. The only thing you can be ruled by is your own intuition. Yes, there are lots of niche markets that may be interested in the stories you want to tell. The problem will generally be getting your book to those markets—especially if you don't have a distributor.
When you're making your decision, stop and think for few moments. There are things to consider.
Will this story paint you in a negative light (meaning, will you dare publish this story under your own name)? Will this story reach its intended audience? How can you make the intended audience aware of the story? If it reaches a different audience, how will they react to the story (meaning, will you become an object of vilification)? Can you handle that reaction if it were to happen? Are you so married to the premise or a part of the story that you can't change it/tone it down to be more acceptable, or would that be diluting your vision? What about editorial/publisher mores? Are you willing to self-publish the story if no other publisher will? And so on…
Doing what you feel you have to do (creating a controversial book) could lead to decreased sales, and decreased sales may mean that you don't at least break even. With comics being an expensive proposition to create, is this something you can truly afford?