Being charged does not necessarily mean you will be found guilty. If all your documents are in order, you have observed the necessary protocols and you have been genuine, you have nothing to fear.
If you feel that your case has been handled inappropriately, then the proper protocol is to either bring it up the chain of command, or via the feedback unit. If these avenues have been exhausted, then you can consider seeking help from your MP.
Beyond this, it is pointless to speculate further on an online forum.
Correct. Only the issuing doctor (or his superior, if in a public hospital) can revoke the MC. The MC after all represents the doctor's professional opinion on the serviceman fitness for duty. The CO cannot revoke an opinion, but he can choose not to defer to it.
MC and ML are often (wrongly) used interchangeably, but in situations like these precision in language is important.