If you have obtained prior permission while submitting the application, they can not reject now. Even if they reject, they should provide such a clause under which such rejection was made. Mere appearing for the examinations is not a crime, and definitely, those disciplinary proceedings are from a different department and may not be connected with your department.
You may ask a friend or relative to file an application seeking laid down norms from Central Public Information Officer, DOPT, New Delhi.
1. Please provide the copy of relevant stipulation/laid down rule and regulations wherein a Govt., a department can bar an employee under suspension from appearing for UPSC examination.
It is left to your discretion as to whether you can succeed further with these charges, even after a pass in the examination. Though suspension is not a punishment, unless the charges are very serious in nature, a Govt dept., can not suspend employee. You may also personally meet the concerned officials to sort out the matter amicably. Think all ways open to you and consult your friends and colleagues.