I am sorry to hear this. Tough situation!
I think when you are faced with this kind of scenario, it will be best to get advice from a good/competent immigration lawyer and/or criminal defense lawyer.
My opinion (I am not a lawyer, this does not constitute as an advice, and so please take this comment lightly) is that it is always best to come clean and be honest with it. You might want to fight off the charges first and clear your name before requesting an FP result. If you proceed with FP and later on IRCC finds out that you have a pending criminal case, IRCC can delay their decision on your citizenship application or decide that you are ineligible and will ask you to wait X years to become eligible again and then re-apply again, at which point you might have to go through another round of waiting 1+ years.
If you have good lawyers and can clear your charges quickly within the 90-day period then that will be good for you. If the legal process would take more than 90 days to clear your charges, then at this point you might have to inform the IRCC about your situation that you will not be able to provide the FP results within the 90 day period. You might want to ask for extension at that point and IRCC will decide if they will give you an extension or not.