AFAIK initialization of ALiVE modules happens on server start. There may be a way to do it but you are probably going to have to do it via Zeus/GM type activity and have that person manually setup the profiles via the ALiVE menu. That way the other force is then going to be active in the server.

At least that is what I have done; but I have also had that same faction listed as a recruitable faction from the start of the server and once they are moving they can add in new members as needed but it is usually a civilian faction.