They pulled Jared Isaacman because it was revealed he had donated to Democrats.
I think it's more likely that Jared was pulled at the suggestion of some staffers that never liked him or Musk in the first place but weren't able to get their way with Trump as long as Musk was still around.
The fact that he was quite competent and generally liked doesn’t matter to Trump, who seems set on defunding NASA and having someone there who won’t complain.