This is "gay friendly" industry without a doubt so the chances of a crew member being fiercely homophobic are very, very slim. Or so one would hope.
Fact is though that the world is full of ignorant and bigotted people to whom the act of two men kissing would cause offense and, in some extreme cases, lead to violence - be it physical or verbal.
Perhaps the way in which the crew handled it was waaaay out of line - indeed, it would seem that way - but two men kissing has more potential to upset other passengers than a man and a woman. Sad (and certainly not my opinion), but true.
None of us can really comment with any authority on this one, for none of us were there, but if the extent of the kissing was merely the very occasional "peck", it should have been dropped. If it was more than that, in the name of a harmonious environment onboard the aircraft, the crew member was perhaps right to approach the couple (though again, not in the manner she did).