I think the question here would be how could he not be removed from his position? As a CO, one of his duties is to lay charges within his battalion where he deems appropriate. NIS do not always investigate sexual assaults; "minor" sex assaults (hate to use the word minor as its not minor to the victim, but merely referring to an assault of such a nature that it wasn't deemed serious enough for NIS) that are investigated by the patrol MPs would have to be sent to the CO if a charge is recommended.
For a person to lay a charge for something he has charges outstanding for is a miscarriage of the legal system. I understand the slippery slope of removing him would be tantamount to stating he is guilty before proven as such, but the reality is if you leave a CO in position when he has been accused of sexually assaulting a minor....whether guilty or not.....the CF will lose the trust of the public.
Actually, the CFNIS has the mandate to investigate all sexual assaults within MP jurisdiction although there have been cases when, due to the nature of the minor offence and/or other factors, they have chosen to wave the investigation to the local MP Det. In all cases though the matter should have been offered to the CFNIS first.
As far as your contention that "minor sexual assaults" would have to be sent to the CO if the patrol MPs investigated, you are incorrect. While patrol MPs cannot lay charges under the NDA (I'll say for now since there is legislation working it's way through the system to amend that and other aspects of the NDA), they can and do lay charges under the Criminal Code. While it is true that there are circumstances where we would proceed through the NDA, it depends upon the level of military nexus and the impact upon military discipline. (Unless the offence was committed outside of Canada and therefore outside of Criminal Code jurisdiction) In cases such as Sexual Assault in Canada, especially when there is a civilian complainant/victim and IF the Base MPs assume the investigation, they go downtown with the charges.
In a case such as this I also don't see any double jeopardy or conflict if the CoC chooses to remove him as CO pending resolution of this matter. Let's face it, he is not losing financially, he would not be losing his rank, he would only be administratively reassigned owing to the pending charges. This could easily be justified because of any bail conditions he may be under, any peace bond conditions he may be under, any weapons prohibitions that may have been sought, the change in his DAG status by virtue of the fact he has pending legal matters.
Regardless, it will all play out over time and I'm sure the media will keep us all informed. I'm surprised Drapeau hasn't been interviewed and provided his expert opinion on it all as of yet.