Sure everyone calls him a faggot and such, but think about it.
He has lived a pretty fucked up life, he killed his own parents when he was like 10, then he spent most of his early teenage years fighting in a war. Now he works as a pilot trying to eradicate war.
He has never had the chance to grow up and learn how to act in a situation like these.
So this guy walks round the corner and some girl who you have never met before leaps at you and kisses you. In Japan kissing is something private you share with someone you care about.
What would your initial reaction be? You are walking down the street and some girl just jumps onto you and kisses you, you would immediately try to get them off you and ask "What the hell?"
With Setsuna, he has never been a social person so his reaction is acceptable.