I've been through this multiple times in the last couple of years, it's worked well for me to move domain authority around in this manner. Maintaining a 301 redirect map on the original subdomain should work fine (probably better than meta headers on reinstated pages, I haven't heard of Google paying much attention to that) and you should be able to claw back your rankings. Running something like jekyll-redirect-from within your old github pages project looks like the ticket. Good luck!