Obviously as already stated by sebsmith in his answer, the two medias cannot be considered canon to each other. We are talking about two different shows, with intellectual property rights owned by two separate entities. Unless some sort of agreement was made, it would be impossible for either of the shows to incorporate elements of the other in its canon.
That said, I would like to add something no one else has pointed out. That actually there have been multiple references in the MLP to Star Trek.
The most evident one is found in the main comic, issue #16. Here the mane six travel through different stories while trying to trap a magical creature on the loose. One of the stories places them aboard a very familiar starship...
... And some time after, Friends Forever #2 managed to do ever better than that. The CMC were still trying to earn their cutie mark and after meeting Discord in the Sweet Apple Orchard they decide to ask him for help, hoping that the spirit of chaos may think up something new "they never would have thought of".
This prompts Discord to create some sort of pocket dimension and make the CMC (who were initially bored by some of his initial proposals, such as lion tamers or fire fighters) go through an increasingly weirder sequence of alternate realities featuring things like The Lord of The Rings, 80's style cops shows, and the following...
(it is somehow unclear if all of those should be considered as realities that Discord created based on info he got somewhere else or should be regarded as alternate realities such as those from the Reflection story arc)
As already stated, both references don't really prove anything and should be considered nothing more than a little nod to Star Trek fans, but it is still nice to know that Discord actually has already crossed the fourth wall at least once to point at his Q "alter-ego".