There is no bar to apply for any govt. job even when a case is pending against you. The reason behind is that the matter is still pending in the Court or you can say it is sub-judice in the Court. If you had been convicted then there would have been a problem for you, because, most of the departments first ask, if you are ever convicted under any law for crime against women or under any other law, or, is there any criminal case pending against the applicant. And if pending then provide the details and status of the case.
In the present situation, you can apply for the post, but you have to mention in the column about the details of your criminal case which is pending and not decided yet. You can't hide these details, because, if later on you are found guilty and a sentence is awarded against you and you have concealed these details from that deptt. then the concerned deptt. can also take action against you for hiding such material information from it.
Hope it helps.