I agree with others that any kind of resurrection will have to translate to either divine intervention, magic, or high tech; so if you are aiming a lot of realism, you can't have resurrection.
If you're looking for a plot device that allows you to revive characters in gameplay while still make believable story deaths, you can sort to nature; like a very powerful medicine that sprouts from specific trees, flowers or forests. It can heal many fatal wounds (the ones from normal battles) but it can't heal extremely serious injuries like the ones from the story plot, or at the time of their plot deaths this medicine was taken/robbed from inventory and there's no close tree in vecinity.
It's still a form of "magic", but the idea is having something that is believable enough ("this could work in real life", explains why it works, and why it can't be used as a Deus Ex Machina), and restricted enough to explain how is it that it can't resurrect story deaths (why it didn't work)
Of course if your game characters die A LOT, it's still going to ring a bell when gameplay mechanics conflicts with story's permadeath.
But don't think it too hard, Final Fantasy VII had both an item "Phoenix Down" and a spell called "Full Life" to revive party members, and still had a major character died permanently in story, and there's a lot of jokes on the internet about that (which is a good thing, that is people talking about your game).