Unfortunately, dead characters have a bad habit of not staying dead unless they're villains. In most every work of fiction.
Massive God Eater 2 spoilers, so don't click if you don't want to know.
In that game, two of the main protagonists die. One is killed by the giant monsters, and your captain later becomes one such monster himself but is sealed away to prevent the apocalypse (it's a long story).
In the updated rerelease, which includes another story arc set after the main game's ending, both end up getting saved with only the main antagonist permanently dying. Your old captain is saved, and the other is brought back with a deus ex machina. There is literally no explanation for the latter - just, you finish the story arc and poof! He's back!
While this game does get a lot of flak for the fakeout death of Nanamo (which still rankles a bit - people don't asphyxiate and then "it was just a sleeping potion, lolz!"), that was the only fakeout death we've really had. The Scions' fates were ambiguous, so them surviving was not entirely an ass-pull and Minfilia is for most intents and purposes dead at this point. Haurchefant and Ysayle are both dead. All of the villains we've crossed swords with, save a small handful (Nero, Regula, and Ilberd), are dead. People do bite it... but we're safe since, according to Alexander, we'll have to make a choice at some point and he cannot see what lies beyond despite having the power to observe all continuum shifts. We're going to decide the fate of reality itself. No pressure!
... but if what you're asking for is branching story paths, well... that's just not economical to put in an MMO. Best to look elsewhere for that sort of thing.