What if... Miko never killed Shojo?

[Kelenius]

The gates as they are now, with even more of them destroyed, have managed to hold for the better part of a year by this point.

We don't know if the ritual can even work at a gate this large. Sealing a rift is what apparently caused Kraagor to die, and that was a small one; and the gates only prevent the rifts from growing bigger. We don't know what is really going on anymore.

With no bargaining chips at all the Dark One would have to be phenomenally stubborn to continue to refuse contact with the other gods

Sounds about right.

it's possible they wouldn't even need to rebuild the gates until after he'd already worked out some kind of deal with them

This isn't very clear. It looks like they'll still need a level 17 cleric to seal the rifts permanently, and there might be no time to raise someone to that level.

As well, assuming the corpses aren't just ashes in the ocean somewhere

They might easily be disintegrated or burned to ashes and scattered. Xykon isn't very careful about his undead.

Locate Object

Range: Long (400 ft. + 40 ft./level)

Greater Scrying

Dead body is an object. And it's been established that you can't scry on dead people.

and Discern Location

That's a level 8 spell, people who can cast it are rare. I'm not even sure if there are any. V just got level 8 spells.