I'm not an author by any stretch of the imagination. I'm simply a reader (and a huge fan of your stories, Com). Even though I'm not an author and don't write, I still kinda understand where this question is coming from. It impacts all types of art (and I do consider authoring fiction to be an art), especially music.
My feeling is that it's better to be heard with some compromises then to not be heard at all. Obviously there could be a lot of compromises given the nature of the subject that's commonly written here at GA. However, if making compromises allows you to get published, and perhaps give you the possibility of making a living dong something you love, then who's to stop you? Once you're an established author you can get more control over what you write/publish.
Personally, I'd say to all my favourite authors that if they had the chance to get published, go for it! It's a once in a life-time opportunity. Do your best to keep the message in your stories as best as possible and go from there.
I could very well be one of the few who think this way though.