As valid as speculation is, we can't tote it as fact--at times we've carried this Magus is Guile idea to the point where we're making assumptions off of unproven assumptions. As blatant as we think the in-game text may be, it's still ambiguous to the point where we're still left in the dark.
It's a possibility, like Justin said, but it's not grounded in cement yet.
Indeed that is true, there is nothing 100% proven that Magus will become Guile. For all we know he could have been place at any point in time, and become anyone he wants.
I personally, wish they did something else with Magus in this ending, ZeaLitY said it the best.
rebuked by Schala and resigned to commit mental suicide is hard to bear.
The long haired, Pale skin, Magus kills himself "mentally".......... (Do I really need to say what that reminds you of?) GREAT, JUST GREAT SQUARE, can you make one game without that? He was always dangerously close before, but now..... Don't get me wrong, the mental suicide fits sure....
O well, he still has one of my favorite quotes.
"If history is to change, let it change. If the world is to be destroyed, so be it. If my fate is to die, I must simply laugh."
- Magus