Currently, if the Master of a Free Company stops logging in there's no way to get that rank transferred to one of the other Free Company members. I submitted a GM Request to get this transferred as it's been over a month since my FC leader has logged in and the response I got was:

Unfortunately, we are unable to assist you with your request since it falls outside the scope of our services.
I think this type of request (with some sort of limitation) should be added to the list of services the GMs can provide players. For instance, if the FC leader isn't subscribed to the game anymore and/or they haven't signed in within 30 days, etc.

Yes, I realize that it's possible to abandon your current free company and form a new one, but as the game progresses and more and more options are added to Free Companies this becomes an increasingly less attractive option.