I thought the Darkstars were gone long before that, around Emerald Twilight.
Actually, after Emerald Twilight, they were apparently taking the GLs' place. The tagline in an ad for the book explicitly made note of it: "The Emerald Light is extinguished! Now it's time for Darker justice!" John Stewart became a Darkstar at the time. And even G'NORT once showed up in a Darkstar uniform some time later!
Were they still an active force in the DCU before Diggle killed them?
Sure. Donna Troy was also a Darkstar, and she was appearing in both that book and New Titans. After the Darkstars book was cancelled, there were a few appearances here and there. One of the members of the InterC.E.P.T. crew that hassled Superboy and the Ravers was a Darkstar. Also, I'm fairly sure that appearance of G'nort as a member was in one of those 80-Page Giants that came out around 1999 or 2000.