I think you're forgetting that the Sanctum 'ok'ed the Purge, y'know the murdering of thousands of people just because they lived next to a fal'Cie because any one of them could have been a l'Cie. Letting in a Pulse citizen who could potentially be a l'Cie with a Focus to destroy Cocoon wouldn't make much sense.
I am talking about FalīCie, not humans.
Humans are afraid of Pulse beings and think they are corrupt.
But FalīCie know they arenīt corrupt but are only enemies.
But Cocoonīs citizens came from Pulse in the first place.