http://www.sentinelassam.com/meghalaya/story.php?sec=2&subsec=8&id=157830&dtP=2013-09-22&ppr=1
As read from above post, the university initially said that they haven't awarded any degrees until May 2013 and a convocation was due in Aug 2013 which probably didn't take place.
As per the governor, 3379 students were enrolled in the University in various courses during 2010–11, 2011–12 and 2012–13, which he has termed as illegal.
As per Section 48 of CMJ University Act, 2009, Meghalaya Govt. will take decision with regards to dissolution of the university after consulting UGC, AICTE and other bodies.
CMJ University Act:
http://megeducation.gov.in/dhte/acts/20-07-09-X.pdf
UGC has most probably submitted it's report to state authorities on 24th Sept. It's apparent from the rejection of CMJ's appeal to supreme court that the university would be dissolved. It's very likely that state govt. would make certain provisions for people who were scheduled to or have already graduated from the university and would definitely make provisions for current students to take transfers to other universities, provided they are genuine.
CMJ and many other universities operated through education consultants who would facilitate any fake degree.
In view of above, CHC is for sure not going to process any applications from students of CMJ university unless State Govt. reaches a decision, which is impending. It's clearly mentioned on the visa application that fraudulent documents may lead to a ban, so it's better to wait.