Yes, you're right. Ballard must have some purpose to the Dollhouse, as a client, as someone who can be used either against the Dollhouse or even for the Dollhouse somehow. I don't think he'll be revealed as a client though from what we've seen it's entirely possible.

I think he'll be made complicit (he already has become personally involved: with his relationship with Mellie he has 'used' one of the dolls though without knowing it.) and will end up in a similar position to Boyd. Adelle has a plan for him and if she's not Alpha's co-conspirator someone else within the Dollhouse has another plan for him.