Ray Smith from Swain's 2012 1AA runner up team is on ECU's roster as a QB right now.
Brad Roach from Williamston's 02 1AA runner up played QB at Catawba, which I realize is D2, but he spent some time with the Ravens and in the CFL, so I feel like that should at least get him a mention.
I can think of a lot of 1A QBs who played D1 football, but a lot of them moved to WR or DB in college (Just in the SMC, JC Brown from Murphy played WR at WCU, Seth Curtis from Murphy plays WR at WCU, Jonathan Shively from Hayesville played WR at App)