The courts have truly been the last line of defense.

Congress being neutered is not an accident, hopefully it will be less fucked if the power balance shifts.

And as the OP is inherently political in what it's calling out, that is not the motivation -- it's the science. I get the fact that in the end, everything's political but partisanship itself is a cancer on the body politic. Just as we seem to be in late-stage capitalism, we are entering late-stage democracy. It pains me that we effectively arrive here by choice.

If Congress wants to earmark that money for a particular purpose it can enact that into legislation. If it wants to empower the executive to make the decision, they can do that too.

Those are the only people who get to decide. Congress can’t turn over the expenditure of taxpayer funds to people who aren’t politically accountable.

Science? Maybe in an ideal world. However, how science actually gets done has always been at the mercy of social, cultural, institutional, and/or economic pressures.

That's a lovely thought but it assumes, as with so many other things about our republican form of government, that the political appointees are good faith actors, at least with respect to funding of science. There are many reasons to suspect that the goal here is not just control of funding, but the defenestration of science more broadly because scientific findings tend to conflict with assertions politicians would like to make. I would submit that people flying on planes, using cell phones and computers, and going to the doctor don't want that, even if they think they do.

That’s Congress and they are.

The executive branch does not hold the power of the purse, and the fact that you can casually use that phrase in reference to the executive branch shows how far we’ve fallen as a country in a decade.

A very sad state of affairs.

Even aside from who manages the purse, accountability doesn't need to mean being able to defend every single funding decision. That would be a sign of bad management in any business, for instance. To me it means competently managing an institution.