This is a very interesting theory. I had also reached the personal conclusion that Cloud's family had originated from Icicle Inn, but had placed the possible migration period a little closer in time - since both Cloud and his mother are blond and fair-colored in general, they would be the last remaining immigrants that hadn't yet mixed with the other darker-haired villagers, maybe?
Your comment about the long-standing distrust of strangers also set me thinking. Both Cloud and his mother seem isolated and poor. Their house is the smallest, if I remember well - I haven't played in a while. Cloud also seemed to be unpopular, and no one defended him when Tifa's father blamed him for her accident (even though he was obviously also a victim). What if he, or his family, were prejudiced against as one of these "strangers" their ancestors had been so wary about?