This is not true. They can also stop him if what he is doing is illegal. Statute can absolutely constrain the executive.
This is an open question. The judicial branch has authority, on paper. But without means of enforcing that authority, it cannot truly constrain the executive.
It's not. Statute has constrained the executive for all of American history.
To put a finer point on it: if the president orders somebody to do something in violation of federal law, and then pardons them, can the law be enforced?
I wouldn't be surprised if trump has in some way violated statute in relation to freedom of speech or academic independence but unless somebody makes a compelling argument that he has, he is a representative of the people operating under the authority granted to him as president, and being a wreckless fool doesn't change that.
I don't particularly like what he's been doing in his second term so far but in online discourse I've seen this worrying trend recently where people think that unelected bureaucrats who were hired because other unelected bureaucrats liked their resumes should be able to hamstring the president and overrule him (i think the strangest thing i've seen was people opining that the CIA should be getting involved). I think it's important to remember that the checks and balances in the US constitution are between the three branches of the federal government, and most of the big bureaus/departments/etc are under the executive branch which he is the sole executive of for the next four years.
The mechanism that Trump is using to deny funding for the universities he hates is through statute. Courts can conclude that this action does not match the statute.
> I don't particularly like what he's been doing in his second term so far but in online discourse I've seen this worrying trend recently where people think that unelected bureaucrats who were hired because other unelected bureaucrats liked their resumes should be able to hamstring the president and overrule him
I'm very sorry, but this is the law. This is not just vibes. If you do not like this, then advocate for changing the law. But you are doing the precise thing that you are insisting that others are doing here.