Fortunately, Kyle never know the truth but I also believe Sean love Kyle heartily and treasure him. It would be more tragic if Yura Tamaki-sensei let Kyle knew the truth. However, it's always better happy ending. (P/s: I am glad that Vinny names his son is Sean & tries his best to accept Kyle's partner)
I believe that Sean loved them both, to be honest.
It's sad that Vinny was the one Sean loved and not Kyle....I feel bad for Kyle. :(