If the Mary-Sue isn't totally self-sacrificing; dying for their love-object; super-intelligent; solving all the cases; getting everyone (male or female) in the lab to fall in love with them; and the writer manages to make them human, believable, flawed and well written, is it such a problem??
But that would be an OC, not a Mary Sue. Mary Sue =/= Self Insert =/= Original Character. Now all three can occur at once, but they don't have to.
Think about it this way--for Zuiker, Nick Stokes is an OC. Is Nick a Gary Stu or a self insert? No.
Of course every character, canon or otherwise, anyone ever writes will have some of themselves in them, but that does not an SI make. That's just unavoidable. SIs happen when a writer either can't write an OC without writing themselves or chooses to put themself in the story (if well done, it can make for some hilarious results.)
Mary Sues are often thinly veiled SIs, but not always. Still, there they are. I did write a story once with an OC that probably could have passed a Gary Stu/SI litmus test, except that he was written in a way that he wasn't the focus of the story and served more as a foil to get the canon characters to think about each other in a different way. I've never been told that he was a Gary Stu or an SI; I have been told that he toed the line, but it was OK because of how he was used in the story.
FF.net isn't...that bad. It does take a lot of digging to find them, but there is much gold and many gemstones in that sludge pit.