Well, I've seen, heard, and watched some friends play TF2 (despite never laying a finger on it myself ^^), and I say this is a pretty good piece! It's funny that these two's personalities match the Engineer and the Spy perfectly...well, almost (Rarity isn't really French). But Rarijack always gets a thumbs up in my book!
Despite the co-creator of Team Fortress 2 himself, Gabe Newell, admitting that he occasionally watches My Little Pony, there probably will never be ponies in TF2, because Hasbro does not want their ponies to be associated with a bloody and violent game like Team Fortress 2.
And as for MLP making a TF2 reference, it isnt as unlikely as it sounds. After all, they had the ponified "big lebowski" characters, and while that sho isnt as violent as TF2, the subject matter and dialogue is much worse. It could happen.
What I think would be interesting is if Meet The Pyro had a reference that was anti-pony. The brony-haters I see around the internet are increasing in intensity, but decreasing in number. They're afraid that Friendship Is Magic will eventually take over the majority of the Internet.
It would be fun to see their reactions on their favorite game being anti-pony as well. Because I've seen what happens when the game shows a love of ponies (Gabe Newell himself admitting he watches My Little Pony caused a massive sh*tstorm on the forums)