"Kissing and cuddling"? It's a plane, not the back row of the cinema! I understand they just got married and are bound to be in the flush of romance, but nevertheless, get a room! Maybe I'm just a grumpy, middle aged old prude.
Either way, I find it really hard to imagine a crew member would say what is written or anything with that implication. I am sure he just said to cool it a little and the Email writer is guilding the lilley. As to accusing BA of corporate homophobia - laughable (as the OP says). Im sure there are homophobic staff, and racist, and all the other 'ists' - it's a big company after all. But it is a long way from that to accusing the whole crew and the whole company of prejudice.