Okay, here's what I got...
In the original Lavos timeline, Janus went into his own portal and eventually became Magus.
In the new Crono timeline, a guy in the Earthbound village mentions that Melchior and Janus both went into portals, again, with no mention of them being together in any way.
Further, when you go back to Medina village, or Ozzie's fort, or anywhere in 600AD, there's no reason to think that Janus didn't still end up in that era, because it's clear the war with the Mystics still happened, and Magus was at the head.
And! Talking to Melchior in 1000AD after the Ocean Palace experience, you think he'd make some kind of mention or something, there'd be SOMEthing, about Janus. (Although he really should have been less 1D at that point, and asked about Schala or something, I mean really... Anyway.)
So, unless you go all Chrono Cross about it (meaning, hey, different alternate realities can just pop into being for no actual good reason, stupid Dinopolis...), I don't think Guile can be Janus and not Magus, unless something *else* occurs somewhere/some-when to cause it. (Not that I'm opposed to that!)
So... I don't know if this is gonna work...