It's also kind of ironic as folks are always saying "characters belong in the MK!". and now, we are parsing out the MK. LOL. I mean we actually have folks saying "characters should only be in Fantasyland!" and it's like - uh, guess we need to dismantle Splash Mountain? LOL. We clearly are way past that point, and it's futile to get all riled up about it because - for better or worse - it's never going to happen - and never really was that way, as you say - the characters have been all over the MK since the beginning.
I do think folks are over-reacting to this - or more accurately, knee-jerk reacting to it - without thinking about it practically and contextually. They aren't thinking past the headline.
What it sounds like to me (particularly with the "upstairs" mention) is that they may put some type of small-scale show/presentation (perhaps something like Turtle Talk-lite), aimed at the kids who really are too young to get much out of Hall of Presidents, in the space above. Which we should actually be happy about because that equals less whiny kids in the main presentation.
If they are appealing to small children, they could invent some character/theme, but I see perfectly why they wouldn't - Sam the Eagle is more than perfect for this sort of thing. It's in his DNA. The fact he is a Muppet is rather irrelevant, really - he's just the most appropriate character under Disney control to do such a thing.
If they were talking a Muppet's overlay, with Sam the Eagle sparring with the Presidents, Statler and Waldorf heckling Ben Franklin, etc. - I'd think folks were being a bit less irrational. But this really isn't that crazy of an idea, and if done discretely/well it could be a neat little thing for both small kids and Muppet-fans alike. And who knows - even though some see it as a low-brow move, hey, if some little kid wants to find out more about history - even just asking "Why is Sam an Eagle?" is better than them not paying attention and asking to play with someone's phone because they are bored.