Whether or not you agree or disagree with the merits of USAID is beside the point. A single unelected and unqualified person must not be given the authority to dismantle a massive US government program.
elections have consequences. We have a representative democracy and administrative employees serve at the pleasure of the head of the administration. "shoulds" and "musts" only go as far as the political will to enforce them. The overwhelming majority of the electorate seems to care about how expensive their personal lifestyle is with various takes on individual liberty vs enforced morality used as wedge issues (neither party is consistently on one side or the other of this balance, fwiw.)
as an institutionalist myself, I agree with you that this is terrible governance.
But he was elected, which qualifies him. The voters voted for this sort of thing. Not in the exact details, but that's why it's a representative democracy instead of a direct one.
USAID was not the only victim.
Did his actions exceed the authority granted to the executive branch which employed him?
Rubio dismantled the program, as the Senate confirmed political appointee of the duly elected head of the executive branch.
You can debate whether the President has the power to dismantle USAID under the relevant statutes. Those lawsuits are winding their way through the courts. But if he does have the power, then it would be perverse if he couldn’t exercise the power due to HR rules. You cannot put HR in the way of the duly elected President exercising his powers.