I think the big no no about bestiality is that animals don't have the same level of intelligence to willing commit to 'the act' which is why most consider it wrong, apart from cross species breeding would have some horrific results for the Child I would imagine. However if they were intelligent, or more intelligent than humans and could willingly commit to it then I wouldn't see an issue, it's like having sex with an alien race in the game Mass effect, sure people might consider it 'weird' but both parties gave their consent.
Thats just focusing on the sexual side however, a massive part as well obviously is whether we would share emotions, the same expectations from a relationship because you have to remember MLP is written by Humans therefore they are 'Ponies' with exact human traits, this wouldn't be the case in reality for example if we found another planet with these ponies on, Yeah I know this is going off the ball right now and really over thinking the question.
Anyway, as for me if they were intelligent as us and shared the same emotions then I wouldn't see an issue besides the physical differences which are quite (no pun intended) large but as in most cases if you love someone enough I guess any physical trait wouldnt matter.