Tell the story you want to tell. If it means ruffling a few feathers, ruffle them.
Don't apologize for your work, and don't hold back in your query. Don't hide the uncomfortable or controversial beneath twisted layers of plot and names and places.
I read a query letter this weekend that showed great promise. Unfortunately, the writer was afraid to highlight the grittier elements of his story. He downplayed them, hid them beneath piles of extraneous details. He was afraid.
Don't be afraid.