After wiping out the Legion at Cottonwood Cove (and retrieving the intel which I didn't on the first visit) and returning to Astor as instructed, rather than being there, the soldiers run off to an encounter with the Legion in which Astor is killed and I fail the Eye for an Eye quest.

According to the wiki, this can happen if you follow the Legion from Novac but I'm going straight from the Cove to Clearwater.

What am I doing wrong?

Happened to me too, he got killed by a Cazador. Maybe try reaching it from another point and beat the Cazador to it?

The same thing occurred to me and I tried walking from CC to Astor via the south side of the town. Fought off three legion and from there I transported back to CS and he got killed by another lot of them.

The second time I carried on walking after fighting off the legion, I continued to walk back and there was Astor alive and well.

So it seems for me at least, the problem was a result of transporting.

Thanks for the reply!