This situation reminds me of the many times I've seen women fall in love with a guy who is Gay-- and they think that if only the guy "tried" to be with them, they would somehow fall in love, and being Gay wouldn't matter anymore.
It doesn't matter whether Sherlock is Gay or Asexual--or even straight--he's simply not interested in her romantically. It's sad for Molly,-- but I would really like to see her move on-- with someone who is not an obvious replacement/substitute for Sherlock.
Another thing: I'm sure many of us have had someone repeatedly hit on us, when we were really not interested in them ..At. All. Most of us will try to be gracious, but sometimes it can get to a point where you're just DONE. And sometimes, that can make us mean. It doesn't make it right, and I'm sure that most of us would just want to crawl under the nearest rock when we've had to tell someone in no uncertain terms that we're not interested-- but there it is.
On the other hand, Sherlock played with Molly's feelings, when he wanted something from the morgue, he flirted. He was nice. He should have known better; and now he's having to live with the fallout. It may take a lot of work on his part to heal that freindship, and I think now--he knows that.