The game never explicitly states that Crono and Marle are dead (unless you assume, maybe, that it takes place in a timeline where Crono never got revived), Lucca's quite probably not dead in Home world, and Frog and Ayla would've been dead anyway by 1020. The ghost-like creatures are not Lucca's, Marle's, and Crono's ghosts. The original cast would've been in their late 30s when they died, and the ghosts are based off how they look when they were younger. The script makes it sound like they're some sort of messaging system that's part of FATE or something anyway.
And, in any case, I'm not sure when "killed off characters for previous game" meant that something was a bad sequel.
Look, is it seriously going out on a limb to say that players were upset more because they played Chrono Trigger when they were young, had incredibly fond memories of it, formed some sort of attachment to the characters in it, and were more upset about the game violating their memories or something and less concerned about the actual merits of CC's story?