Yes, unless they're changing that in the new version or something. I hear that FES lets you prevent the death of a character that died in P3 original, so I guess anything's possible.

If you maxed out Shinji's S-Link before the incident, FeMC will end up saving him. He's not playable for the rest of the game though. And I think this only applies to the FeMC side, not Minato.