(Disclosure: I am heterosexual, so be aware that I might not be the leading authority on this sort of issue.)
Let's get one thing out of the way first: the inclusion and pairing together of Bon Bon and Lyra must have been done with some awareness of how they're often paired by the fandom, and therefore of exactly how the fandom depicts their relationship. With "Slice of Life" being chock-full of fan service as is, it's incredibly unlikely that the writer, M.A. Larson, was ignorant of this, especially given that he's possibly the My Little Pony writer with the closest links to the fandom. Therefore, the decision to put such emphasis on the two being "best friends" was a conscious decision, and while it's likely one made in jest, it's also one that gives legitimacy to homophobes who refuse to see any non-heteronormative relationships in the show, and while children aren't dumb, it's possible that a fair number of them might take it at face value. Now, at face value you can get the impression that Studio B fit what they could without hypothetical backlash, but season 5 director Jim Miller has gone on record denying that the two characters are romantically involved, which punctuates how the scene can easily be interpreted as completely platonic by those who would wish to. Therefore, it can't be regarded as representation of LGBT people in the show.
Whenever I've suggested on Twitter that Larson should have just made them explicitly a couple, however, I've been consistently met with people thinking that religious fundamentalists and moral guardians would cause a stir. A counterpoint may be extrapolated from a point raised in Pony Palace's review of the episode, written by Whammy, wherein a comparison is made to Steven Universe. I haven't seen Steven Universe, but Whammy brings up that two characters in that show have developed a relationship that is very hard to see as not romantic, and it has to be considered that this is a show which airs on Cartoon Network, the single most popular channel for children's cartoons. Of course, Stephen Universe isn't as well-known a brand as My Little Pony, but it appeals to the same demographic, and that Stephen was willing to make such a move reflects badly on MLP. You know what is a popular brand, though? Avatar: The Last Airbender, and therefore The Legend of Korra, a show that ended with two female lead characters sharing a romantic moment. Korra may skew older than My Little Pony, but it also aims broadly enough to include children and airs on a children's show network, and there are no reports of Nick or Cartoon Network coming under heavy fire for the depiction of these relationships.
Even considering the potential reaction of religious fundamentalists, it's important to note that progress isn't made by listening to reactionary voices. Having a major brand like My Little Pony make steps towards representation would be a huge step forward for the medium and provide a great example for children who, again, might not get that from the route that was ultimately taken. Hasbro has made steps towards progress in other properties. For example, the Jem and the Holograms comics include a homosexual relationship, as is explicitly stated by their creative team. However, the comic of a less popular property wouldn't have the same impact as My Little Pony would, and while they could have gotten away with ignoring the issue, the inclusion of Lyra and Bon Bon with such subtext brings that show's reluctance to face the issue to the surface. Another popular argument goes that the show, being called Friendship is Magic, shouldn't include non-platonic relationships, but considering that heterosexual romantic relationships have frequently made appearances in the show (to the extent that there have been two marriages), that argument really doesn't hold water, especially considering that Lyra and Bon Bon are not main characters. I can't emphasize that last point enough: Taken in a vacuum, having the two be in a relationship would have no meaningful impact on the show, and hence wouldn't be any different from the straight marriage that was the episode's framing device. Besides, putting a character in a relationship isn't nearly as drastic a change as making one of the lead characters royalty.
There is one argument that may hold water, though: My Little Pony airs in several countries across the globe, some of which have cultures or laws which oppose homosexuality. I don't think that was the reason that the two characters' relationship wasn't explicitly stated, but it could be a justification for it, no matter how disappointing it may be. Sure holds more water than fears of moral outrage in North American markets, wherein the tide is increasingly in favour of same-sex marriage. Even considering the limitations that those markets may place upon the show, however, what is clear is that My Little Pony's decision not to explicitly state Lyra and Bon Bon's relationship is a huge missed opportunity for major progress, and merely enforces a heteronormative view in its own universe. Stacked up against other shows which have made greater leaps, that's a huge disappointment.
(To be clear, I actually did find the Lyra and Bon Bon scene very entertaining.)