Having read through a healthy chunk of this thread I would like to throw in a brief opinion.
Some may be confusing the issue of biological normalcy/abnormalcy with social mores and morality.
Saying that homosexuals shouldn't be televised because they are biologically defective is illogical, because we already show other biological "defects" on TV and kids TV all the time. People who need glasses or who are blind? That is a biological "defect", but one with no moral stigma attached. Same for someone who is going bald, or someone with hearing issues, albinoism, etc etc. But none of those people have the same kind of social stigma attached to them as homosexuals (yes, I know that culturally the disabled have a much harder time of it, but they aren't viewed as evil and vile in the same way as gay people. That is another discussion).
So, there are only 2 real reasons not to show homosexuals on cartoons, and that's due to 1: Being uncomfortable showcasing any aspect of sexuality or romance to young children or 2: Anti-Gay bias (or the "OMG yer trying to turn my kid into a queer" panic).
#1 is perfectly understandable. Some kids will be too young, some shows aren't set up to accomadate that sort of topic (re: barny the dinosaur, shows aimed at primarily preschoolers, etc).
Some shows however are aimed at a more middling audience. They have jokes in them aimed not only at the younger children but also at the more mature crowd - Animaniacs etc when I was growing up, and seemingly Ponies now. They already have romantic content (even if it is only the most rudimentary form of it). So what's really wrong with having any references to homosexual attraction in a show that already has aspects of romance as part of the sub-plot? Young adults (part of these shows target audience) already know about gay people, already understand crushes and romance (however ill developed these notions are at that age) and are already starting to form opinions.
I'm not saying it needs to be over the top, or blatant, or thrown out there as a major plot point. But why is there such a resistance to even a hint of it on a show that already has romantic subplots?
I think that brings me to #2. And really people, arguing #2 is a valid reason is like saying that racism is a good reason not to have black people on TV, or that sexism makes it ok to NEVER show women being strong and self reliant. Backwards and ignorant.
In the specific case of MLP - it seems that an overarching message of the show is "Accepting people for the differences" Why not have 2 girl ponies have a little crush, just in passing? Hell Spike's been heart-eyed for Rarity since episode 1.

Or 2 boy ponies (there aren't a whole lot of those in the main cast though so...)