The executive branch's ability to simply de-staff and de-fund organizations whose existence is enshrined in law seems like a clear imbalance as far as the separation of powers goes. Effectively a line item veto of sorts across every aspect of government / law. A magical power that only the executive branch is being granted (coincidentally only when the executive branch's political party matches the majority of SCOTUS).

Does congress pass a law that says for an agency to do a thing with a veto proof majority? Doesn't matter, executive branch can just choose to de-fund and de-staff it ...

The fact that SCOTUS indicates they're not making the final call on this right now seems to simply play into the hands of those who don't really care to follow the law anyway.

It's doubly strange that with a single party now controls congress and the executive branch and they clearly have the power to actually change the law utilizing many other elected representatives who are presumably responsive to the people ... the executive branch is still granted this extra power to simply ignore the will of congress.

To be clear I think nobody in the executive branch, of any given party, independent, or otherwise should be granted these powers. Same goes for the magical immunity granted Trump not long ago. If anything the executive branch and those in power should be subject to far more legal scrutiny.