No, Obama did not suddenly make Touch 106.1 legal. He didn't waive the process of applying for a license. None of which, Touch has done.
Also, do you really think "thanks to Barack Obama" that he knows, cares or even gives a rat's ass about a 100w pirate station in Boston?? I would think that North Korea is a larger problem on his plate right now.
The reason Touch exists is that the local politicians have told the FCC "hands off" because of who they are.
There's also no reason a 501(c)3 organization can't be running an illegal activity. Happens all the time.