Hi, I work at Stripe. We are actually now able to support Puerto Rican businesses. (We need to update that support page!) Shoot me an email at edwin.wee@stripe.com and we can get you set up.
The limitation seems completely arbitrary or stems for a misunderstanding about the difference between a state and a territory. For better or for worse, Puerto Rico is virtually a state (with residents who can't vote for the president with some minor other caveats), but legally there shouldn't be any difference.
