An article recently posted here on HN gives a more nuanced explanation for what's going on: https://news.ycombinator.com/item?id=15807842
TL;DR, the tuition fee deferral scheme that universities currently use is a grant-money laundering scheme. It's used to take federal grant money that comes with strings attached (e.g. can only be spent on certain things like paying salaries for grad students, or research costs) and launder it into money that can be spent on whatever the university wants (e.g. building new campuses or paying for nice desks for administrators). It's probably not unreasonable for the federal government to try to close this loophole.
The issue is that students are caught in the crossfire here, and I'm not sure that the incentives are there for universities to protect them fully.
But to be clear, the universities could just stop billing the government false grad student salaries, and then grad students' take home pay and tax exposure would remain unchanged, and there would be no crisis. The problem is that then universities would have to find a new money laundering scheme, or would have to make structural changes to their budgets that they would prefer not to make.