So I have a theory on the timeline here.
There are three points that I think are worth keeping in mind:
1: Borek, by all accounts, didn't think that Karak Dum had fallen when he started this expedition.
2: The very second he took a look at it now, he thinks they need forgiveness from the Ancestors.
3: Most crucially, Borek did not seem surprised to see Morghur
I really do like the "Morghur was born into a Karak Dum family, who managed to runically contain his nature" theory. It's a theory that's fully congruent with what we know is possible and it is fits with BoneyM's stated views that anyone can be redeemed. The problem is that it in at of itself doesn't explain why Borek only thinks Karak Dum is beyond saving now, when he clearly has to have known Morghur's existance from before he left it. Something has to have changed between the two points, and we do have to do some finagling -and indeed some blatant guessing and assumptions- to make it fit, but I think it can be done.
So what I think could've happened is this:
Before Karak Dum got swallowed up by the Chaos Wastes, Morghur got killed in Bretonnia and got "reborn" to a family in Karak Dum. Since Dawi are notoriously resistant to mutations, the actual "growth" of Morghur got slowed down enough for Karak Dum's runesmiths (renowned as among the greatest) to be able to develop a way for pre-Morghur to retain his sanity and literal grip on reality as he grew up. This is not inherently different from what the rune of Valaya does, so it is not an impossible feat to imagine. The dwarves of Karak Dum now had a fully sapient and very powerful Beastman living peacefully among them, a fact that they chose to keep secret because let's be honest, the vast majority of Order factions would not believe for a second that this could actually happen.
So now Borek leaves Karak Dum, which notably was still part of a mountain range at this point, to make sure help actually arrived for the oncoming Chaos Storm. Probably with a tearful goodbye from Morghur, because that's how fiction rolls. And the warning was not heeded, Dum got swallowed up, Vlag disappeared, Borek swore vengeance and the rest is history.
Karak Dum then spends somewhere between 20 and 200 years under siege from the Chaos forces, where Morghul naturally participates in defending his home. The scene seems dire and impossible (because it is), and so the Dawi decide to go radical. Using the genius of their runesmiths and bits of ancestral beastmen knowledge stuck in Morghul's mind, they manage to make their waystone appear and/or act like a non-corrupted herdstone. Which is what made the Beastman forest (that Mathilde described as disturbingly familiar, which means it is similar to Imperial forests in some way Mathilde can't explain) appear in the mountains, where a forest of that type wouldn't normally be able to flourish. But since that isn't enough to ward off Chaos forces, I think what they eventually did is rely on Morghur's metaphysical nature as a world-altering demigod to either attract beastmen to their cause or to turn themselves into something beastmen like. Which are obvious enough ideas as last-case solutions that they were probably discussed before Borek left, and that he then recognised on sight once he got here.
