state.gov is not a reliable source, naturally they won’t say the truth or even their actual intention or reasoning. Recall the DHS has made up lies and deepfakes about just about every victim killed by ICE on camera.
Then you linked to a state.gov document that lists numerous anti-Israel and pro-Palestine activist groups used as justification for a terrorist designation.
Did you even bother to read this document, or did you just CTRL+F "Israel" and miss all the times Palestine was mentioned?
Not sure why you're hyper-focusing on that one section and deciding that that was the motivation for the designation when there are plenty of other bad stuff happening there that more than justifies it. Besides the fact that many of those groups do indeed support terrorism.