Guile isn't the Magus. It's just the truth.
However, if Guile (or Alf) were connected with the Zeal Royal Family, I'd suggest an alternate idea... that he'd be Janus, but not the Magus.
After Crono and his friends invaded Ocean Palace, I recall one of the survivors (perhaps in the Last Village) describing the whisking away of Janus and the Gurus into Gates. During the flashback of the original event, all four of these people were taken into different Gates. This time, however, it seems that Janus and Melchior entered the same Gate, leading to the possibility that Janus went to the 10th Century instead of the 6th, leading to a whole different life for him. Thus, a mysterious, magically gifted young man in the 11th Century could be Janus Zeal and yet have no memory of the doings of the Magus...
Of course, that has nothing to do with this discussion, when it comes down to it.