I believe the game may have some issues with event sequences. Specifically for this case: Darkhammer.
During my game I suppose I went off the tracks unintentionally and dedicated myself to the removal of the xenos causing havok across the map before dealing with the Great Enemy itself.
I killed Darkhammer to secure the alliance with the Eldar, and then went on to kill the Abaddon's Tzeentchian follower. After this, I received a transmission from the Dark Angels, helped them and sided with their Chapter.
After the mission, Darkhammer reappeared to comment on the events of the mission with Spire. Despite the fact that he was long dead.