Leonard was never over Penny. Leonard was still with Priya in that ep (until the Skype chat at the end) and he had all intentions of staying with Priya because even though he loved Penny with all his heart, she pushed him away. He had no clue she was feeling what she was feeling...and I hope one day he finds out otherwise.

That ep was written (and this is just an opinion here) to prove that Leonard is a good guy (because he couldn't cheat on Priya) and that this is proven not only to the audience but to Penny. In the end, his heart gets broken by Priya, however that heart break put them back together and that's all that matters.