That's not entirely true. They were asked to put up collateral and then banned from accepting new federal-aid-dependent students because the DOE received word from ITT's accreditor that ITT's accreditation was at risk due to, among other issues, ITT's financial status.

Now, among the sources of the problems for ITT's financial status were the SEC and CFPB fraud lawsuits themselves, and, IIRC, changes in ITT business practices that were taken in response to those lawsuits. But the primary direct trigger for the DOE actions wasn't DOE's evaluation of ITT's financial status, but the risk that ITT's would lose its accreditation, which would make it ineligible to enroll any students accepting federal student aid (not just new students, but continuing students as well.)

Sometimes, to prevent further damage, a court may decide to freeze assets or prevent a certain activity while the case is worked out. But that's the job of a court, not an agency like the DOE.