I saw that as more a thing that every time Sheldon makes a lady friend (Stephanie, Dr. Plimpton, that other old lady, um....even Leslie to a small extent, Penny), she usually ends up in bed Leonard. I can see Sheldon finally snapping over that, seeing the possibility that had things gone a LITTLE smoother at that wedding (i thought Leonard and Amy had some great chemistry to the point that I wouldn't have been surprised if they'd ended up in the sack), she would have, too. Thus Sheldon hit him, as a "she's my friend!! not yours."

I just can't see him as having underlying romantic feelings for her. But as a friend, sorta? Sure, and thus him trying to keep Leonard from "corrupting" another lady friend, as he's done before.