It is hard to say for sure, but of one thing, I am certain.
Magus's search for Schala is completely uncompromising, to the point I'm not actually sure Magus knows what he'd do with her once he found her. Tell her he's Janus? Sure. Hold each other awhile/cry/fanfic drama? Yeah probably. After that... what? It's a variation of the journey being better than the destination, in a weird sort of way. It gives him purpose in life... but I digress, point is, he is ridiculously dedicated to it, even if it ultimately succeeds yet he fails to save her. Wiping his own mind and becoming Guile in order to continue searching for her "correctly" is, in a sort of paradoxical way, the only way you'd get him to stop (and this is assuming Schala didn't just pay Guile a visit and fix it up somehow anyways)
There's a lot of both games that have been on my mind as far as what wouldn't be a completely cop-out or cheap shot in terms of a potential continuing story. I'm debating actually writing this down somewhere at Compendium.