Be careful what you wish for. Endowments and foundations aren’t really accountable to anyone and just end up getting taken over by people with their own agendas.
It's true. While we're complaining about his sister, we could easily be complaining about someone who came into power of a well-endowed foundation with an agenda we don't like. It doesn't take too much imagination to, say, imagine a climate extremist who blames all computers and cyberspace for consuming so much energy and destroying the planet.
One friend who toured Montechello recently said that there's so much emphasis on slavery that the house has been turned into a monument to the bad things that Thomas Jefferson did in his life. I'm not saying this is incorrect or bad. Only that I don't think this is how Thomas Jefferson imagined his house would be used after his death.
I have a hard time seeing how that's a worse outcome than Monticello (or the computer collection) not being preserved at all (which seems to be the implication of "be careful what you wish for"). A museum agenda you disagree with can be changed in the future by new management, but once the artifacts are gone, they are gone.
A historical site like Monticello needs to be preserved in place, but when it comes to museum collections, a lot of times it's just as well for stuff to end up in private collections. Collectors tend to care (sometimes to an obsessive degree) about whatever it is they collect; it's not just a job for them, nor do they get possessed by weird ulterior motives the way foundations can be.
As someone who has been on the periphery of non-profits for years, they easily become mostly employment sinecures for executive directors and others. I've actually seen foundations set up to formally wind down operations after some number of years for exactly this reason.