Bounty Hunter ID can work in place of Freelancer. Once you think about it, in the actual game what are you hired to do? Blow up ships for money. That's more of a bounty hunter then an actual freelancer.
Now, if there were a Merc ID, there would be a few more options. For example, a Merc could be hired to protect someone, bolster some forces, perhaps help train soldiers, or even play scout for a main force. Those with Merc ID's can play individual mercs or could even create their own Mercinary Company.
Say you created a character named Massako. She works in special ops, then retires. After a while, she decides that a life of luxury isn't for her, and starts looking for good troopers to start a mercinary company. Thus, Massako's Marauders are born, and quickly establish a name for themselfs as the most ruthless and perhaps even one of the best equipped ground forces on the market.
With the Merc ID, however, there would come some limmitations. For example, something no Merc would ever do is go back on a contract, no matter what the "other guy" paied. The Merc does that, and is never hired again or even killed by the second employer. Once the contract is paied out, that's an open question. Then the question of ships becomes important, as no government is going to sell someone their battleships and cruisers. They might make use of armored transports with vastly imporved armor and weapons, or use the Container Transports (Due to the large number of guns) to land entire companies of troops at once. Use your imagination.
And, to actually answer your problem Quin, the Bounty Hunter ID is your best bet to keep a Freelance character. Beyond that, I would say the Neutral ID.
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