Well its purely speculation on my part in regards to Merlin. The UK
is light-years ahead of US in this area that said I've seen racism in both UK and US fandoms very recently. There was some very strong race based hatred aimed at Freema Ageyman during her Dr. Who stint and don't get me started on True Blood.
I think you're right, I doubt it would affect the show, TPTB appear to be committed to this storyline which is awesome IMHO.
I was thinking it could just cause some stress on the actors. Sometimes male actors also get weird about romantic leads or what they perceive as being an overly strong reaction from female fandom. Roger Howarth was totally freaked out by female reaction to his character on One Life to Live.