the (politically helpful but rather sketchy - talk about your Deus Ex Machina, too!) Vorlon ship that blows up Deathwalker's vessel

I wouldn't call it Deus ex Machina - it is consistent with Kosh's absences from the council, which are commented upon in the course of the episode.

it's more shades-of-grey than Trek usually goes for

The nature of the scenario reminded me of Star Trek, too.
The whole thing feels a bit like a Trek dilemma done differently.