I think that if Harry and Ginny hooked up, it would not hurt Harry's friendship with Ron, because Ron seemed to favor that match (a book or two back). So I think after a little readjustment period, Ron would come around. However, I think even though Harry and Ginny are drawn together, he may find himself having to distance himself from her to protect her from being used by Voldemort and his Death Eaters as bait or a way to capture and kill Harry.

I know it's a sad thought, but distinctly possible and (sadly) par for the course in Harry's already tragic life.