Maybe it's because of Roosevelt's controversy?
His controversy may have kept him off the show for good (aside from some non-speaking background appearances, at least one of which ended up being cut), but Sesame Workshop doesn't avoid acknowledging him.
Episodes featuring him didn't cut him out on Noggin, DVD, or iTunes (and I admit, I don't know that this was never the case with Roosevelt on those formats). Sesame Workshop has put out a number of his clips online (though only two where he was a featured character). One of his segments was chosen for inclusion in 40 Years of Sunny Days. He's often talked about in books celebrating the history of the show. He tends to be included in anniversary merchandise (there was some official artwork of him for the 35th anniversary, for example). Palisades Toys planned on making a Roosevelt Franklin action figure for series 2 of the canceled Sesame Street action figure line.
And besides that, I don't think the dead Muppet wall (or was it "dead puppet wall"?) was open to the public. It was just in one of Sesame Workshop's buildings, basically a lounge. And besides that, it would have just been a picture of him. I don't think people unfamiliar with the character would look at a picture of Roosevelt and instantly think he's offensive.
I don't think that wall's around anymore (at least not as a showcase for characters no longer on the show), but it would be great to see pictures or video footage of that wall (assuming such things were allowed). Though it was said that they'd remove pictures when certain characters appeared on the show again. I know this is a topic for another thread (is there one?), but I'd still like to know who all was represented.