Probably allowed, I dont see why it should be forbidden.
Especially if one of hte factions is supposed to be kinda secretive, like the Order.
Order has undercover agents all over, allegedly.
Of course, you'd have to stay consistent in who knows who you are and so on to stay consistent. but bad RP can be bad RP on a single character too.
If you got an Order character and the navy knows his name, dont be surprised if the navy will also treat your Freelancer/zoner character as an Order agent if he has the same name. Being surprised about that is really the only problem I could see here.