Why do we still have people on the battlefield?
Because without people the enemy will keep on popping up. Perhaps one day robots will take over entirely, but it will mainly cause the hatred against you to set deeper. And war, as much as *cough* some people *cough* choose to ignore that fact, is in essence very, very human.
The counter to these frigates will likely be reminiscent of the "tipping over" of V1 flying bombs. Since there are no people around to repel boarders the latter might simply disconnect the AI and receivers, put the thing on a nice circular course, and carry on. Or maybe they'll sell it for scrap, or use it to tow contraband, or what-have-you.
On another note, we are already waging a robotic overlording war on people so backward they haven't caught on to "9/11" yet and don't know any better than that we're just attacking them because of their beliefs -- and no local lord will disabuse them of that notion even if they do know better. Long term, we're setting ourselves up for a nice fall.
I see what DARPA is trying to do here, and that's fine, it's what they do best. As an instrument of policy however --as military vessels tend to be-- it probably is a less fortunate choice.
Maybe as an automated cargo barge to slink past Somali pirates?