Suppose the amnesiac Magus is not the 2nd one, but he is in fact the one from your party? Therefore Schala was attempting to protect Magus from trying to go after the Devourer again, and at the same time nullifing the 2nd Magus' actions that we see.
Also, the 2nd Magus is clearly from the normal post-Trigger timeline. He goes off, finds a way to enter the Dimensional Vortex, and there we find him. Of course if the amnesiac Magus is the one from your party, then this changes his future, in that he wouldnt have gone after the Devourer, unlike the 2nd Magus. Sample timeline:
Ending of Trigger, Magus 1 and Future Magus goes off searching for Schala -> Future Magus goes into the Dimensional Vortex, where we find him -> Magus 1 Enters the Dimensional Vortex also -> Schala wipes Magus 1's memory -> Future Magus ceases to be, because Magus 1 would not enter the Dimensional Vortex, and therefore not have his memory wiped -> Magus 1 ditches his scythe, cuts off his ears, moves to El Nido and is Guile. (Yeah right.)
In short, although having Magus 1 be the one who loses his memory is interesting, it is way too problematic to work.