Yeah, Rin does not like Molly that way:
Which they both knew since before the game started, apparently.
However, if Rin wasn't adverse to those similar to herself, they might have had a decent relationship, tbh. I don't really see much problems for them beyond Rin's lack of desire for Molly.
Edit: Plus Rin could have always just tried dating Molly anyway, if Molly actually confessed to her instead of ignoring Rin's feelings. Maybe learning to enjoy eachother more than they initially thought they would. At least in Rin's case.