She didn't tell him she felt unappreciated in LotTL; she told him she couldn't take being around an unrequited crush.

She told him she "spent a long time feeling second best", or words to that effect. That's about more than the crush.

(And no, the Doctor's not morally obligated to reciprocate. He is morally obligated not to be an utter arse about it, which he is when he uses the unrequited love analogy for the perception filter -- after the end of Family of Blood there is absolutely no doubt that he knows.)