Urien was brown, alive at the end of SF3, and wasn't the only person with a gem.
It's just as likely that it was Gil/Urien who brought Charlie back and sticking one of those gems in his forehead is part of the process.
And by just as likely I mean there's no actual reason to believe any of outside of random ass speculation.
Wouldn't be surprised if the story is about bridging the gap between shadoloo and Gill. Having Gill resurrect (see what I did there?) Charlie and send him after Bison doesn't sound too off from what could happen.