Hmmm....Ever since the PSX release came out, it's definitely a debatable thing on what may have happened regarding Frog/Glenn....Since the point of the SNES version has already been said, I won't go any further regarding that part.
Now I'm sure that most of us are aware that Guile was originally intended to be Magus in disguise in the events of CC. So Square was definitely intending (well, at first) to keep Magus alive after all the events of CT. Of course, we know what happened with the Guile part. Now in Lucca's letter to Kid, we know of the "Hello Janus" part.
I see this as one of two possibilities. This was originally scripted in CC during the whole "Guile is Magus" point in developing the game and that part was overlooked in the final review before SE released the game to anyone. And of course, we know in the past, plenty of games have had either script and/or translation goofs for one reason or another so that's why I leave this thought open.
The other possibility (as has been reviewed on here) is that Magus did at one point travel to 1000 AD (or maybe somewhere inbetween 1000-1010 AD) because he learned of Kid's existence (maybe even through Lucca). The possibility that Frog maybe traveled to this era again at one point or another or he may have left some kind of letter/item that may have benefited Magus (possibly due to that he knew Magus would be back to that era or maybe even the Middle Ages). This may have left an impact on Magus to where he may make amends with Frog and change him back to a human.
Getting back to Square's intention of Magus, maybe they didn't intend on leaving Magus alive for some reason. As we all know, Magus was an optional character to have in CT, so that could maybe have something to do with why they hacked the "Guile is Magus" part of CC. And of course, note that in the PSX version of CT, Magus does not have any kind of FMV ending but that of course could also be due to Magus being an optional character in the first place.
But of course, as stated, maybe Square was just too damn lazy to make a separate FMV for Frog.