As I'm reading these posts, I'm feeling some new hope for the OC's that I'm writing for my various fanfics. My beta even said the same thing, that most people view an OC pairing up with a canon character as a Mary Sue. In my opinion, I think that as long as the character is well written (has flaws, etc.) then the pairing could be plausible. That's why I try to pick canon characters who haven't been paired with another character to see what I could make work.
I make sure to do my research ahead of time and plot everything out that I want placed in my story. Doing this helps me to make sure that I don't make the characters OOC, even though I'm placing an OC in there. Being a fan of said show helps a lot, as well!