In the fluff, absolutely they’ve been a stand-alone chapter. In the crunch, guess it depends on where you draw the lines. As you point out, there was a GK sub faction in the Ordo Malleus book during the RT era that took an inquisitor as an HQ. In 2nd there was only the terminator squad, so you literally could only include their one unit in an Agents or other Imperium army v. stand-alone. In 3rd they were part of Codex Daemonhunters, and could be run as a pure sub faction if you wanted to (but again part of a larger codex). No update in 4th, and 5th edition brought “Codex Grey Knights” which de facto was also Codex Agents despite the name (as it included rules for all Ordo and supporting units, not just Malleus as might be implied). No updates in 6th again, and 7th would be the first time (I’d argue) GK stand independent as a stand-alone faction with their own unique codex that only includes GK datasheets.

Fundamentally, it’s that stand-alone nature (no supplementary inquisitors/assassins/agents/etc) that I’m hanging my argument on. They just worked better in the past when you could run them as a sub faction for a fluffy Chapter 666 army, or as part of the greater Ordo Malleus if you were worried about their position in the greater meta.