When asking for letters, you should ask if the prof feels he can write you a supportive/strong LOR. In a better world, he would openly decline to write it if he couldn't w/out prompting.
I had a science LOR from a professor in whose class I received a B- and one from whom I earned a B+. When I requested these LOR's, the writers told me what the shortcomings of my letter would be...but they typically know how to spin the wording anyhow...i.e. "this student only has an average grade, but this course covers unsually rigorous material very rapidly and is curved among extremely competitive, motivated pre-medical students. I feel that this performance reflects more than adequate potential to succeed among these peers in medical school" and hopefully something more personal. So, it might not all be sunshine and moonbeams, but it's not necessarily too bad...especially if the alternative is to get one from an 'A' prof who can't actually say anything about you as a person.