It does not depend upon the gravity of criminal offence. The probationer cannot be removed from service simply because a criminal case is registered. It will amount to shortcut of disciplinary proceedings and violation of CCS(CC&A) Rules and overstepping of CS(TS) Rules.
The query is silent about the timing of probation period and date of discharge. However, at the time of clearing of probation, vigilance clearance is required. If a criminal case is pending (regardless the gravity of offence) such clearacne is not given and the person (regardless the performance report) is liable to be discharged.
In this case the person was already holding another permanent post from whcih he came on technical regisnation and till confirmed in present post held a lien on past post. So new deptt could , even if he does not complete probation cujld revert him back to same post.
EIther the queriest does not have full facts. Or a gross miscarriage has been done.