It is because Trump is doing most of these things through executive orders and presidential appointments it is up to the judiciary to strike them down, not the congress.

To make this stuff permanent they would need to go through congress, then it is much harder for a future administration to repeal these changes.

Same deal, the judiciary could smack him down, and is to an extent, but the extent to which they aren't is down to them not wanting to. The checks and balances are intact, merely choosing not to check and balance as the democratic party wishes they would.

Congress could do all sorts of things to assert its power: it could call hearings, issue subpoenas, revoke or change appropriations, pass laws, file suit, threaten impeachment, actually impeach. The courts could get involved if the administration resisted or defied some of those actions too, of course.

They have no interest in doing any of that, though. Generally those in power in Congress support what Trump is doing and are happy to have it happen without them needing to lift a finger (or take the blame if there are problems). To the extent that they don't, they're also happy to rely on the courts and again not take the blame or blowback from their voters.

As the administration plows forward and gets a taste for operating outside the law, I do think you have a growing risk that even a Congress that wanted to resist would find itself unable. You see administration figures favorably citing arguments that they should ignore court orders even now, and some evidence that they're defying orders already.