What I've heard several times is some version of the following. Although none of the particular sources were all that reliable, I've heard it from enough different sources that I believe the basic outline must be correct:
1) the Treehouses can't be used as guest areas because they are not handicapped accessible. They were built before the ADA, but eventually that grandfathering ran out.
2) Disney might be willing to spend the money to make some of them accessible (ADA doesn't require all of them be accessible), but apparently the fragility of the ecosystem, including the fact that the trees themselves are now protected, makes construction not possible.
3) However, they CAN be used for internal purposes, so some lucky CM's do get to stay in those wonderful accomodations.
We can only hope that something happens to allow the treehouses to be used for guests again. I stayed in one when I was a teenager, and it was really a great place to stay.