If we're building ships to fight Sathanas threats, I've got one grim justification for cruisers in my head.
In a white room, just tabled stats, fleet vs fleet fight, if we assume a Sathanas has no delay from switching targets but can't switch a beam's target mid-shot, then it should a collosus in 40 seconds, or kill two destroyers every 10 seconds,or kill 4 of anything smaller every 10 seconds.
We can't really know how the costs and manufacturing capability break out, but if going just by a very crude estimate of volume then a destroyer is 'worth' around 25 corvettes, or 470-ish cruisers. It seems unlikely that it's a simple switch between "build 1 destroyer" and "build 500 cruisers", but dozens certainly seems plausible to me.
So, if you are planning for the possibility of having to fight a fully-fanged sathanas, cruisers start getting attractive because it can only kill them so fast, and when it does you lose a lot less than you would with a larger ship. It requires you to abandon the idea of your crews not being expendable, and there's a lot of other factors that muddy the waters, but I do think it's a plausible thread to pull on.
I do think there's also out-of-battle utility factors to consider. A cruiser can loiter, it can show presence and provide some measure of security. Yeah, fighters can do that some, but there's got to be a limit. The fighters have to go home after a few hours, the cruiser doesn't. And yeah, corvettes, but cruisers existing is easily justified by simply saying they can't afford as many corvettes as they'd like, and need cruisers to fill the gap. Sure, it'd be nice to just have bigger, better ships everywhere, but sometimes you just have to settle.
They can be needed for the fleet's overall operation, and still go up in smoke the minute a bomber wing or shivan cruiser notices them, that's not exactly a contradiction. At least, not the kind of contradiction that would stop a military for doing something.