I don't know if the idiom exists in English, but in my native language you are considered "orphaned" once you lose your parents, regardless of how old you are. That's different from actually being an orphan as in losing or never having your parents since childhood, of course. In my mind, he is orphaned in the sense that he's lost both parents and has no parental figure left.
....which actually fits in really well with my long-standing headcannon that he latched onto Meredith as a substitute parental figure, so it turns out this new!new turn of events works more for than against me, in the end. Huh. Of course. He lost his parents in the Blight, he went through all that mess in the Circle, he had to leave Ferelden and the family he had left there, and in comes Meredith as the mentor/authority/substitute parental figure. It's perfect.
Anyway, I digress, lol.
I vaguely remember Cullen mentioning that his "family" moved to South Reach, implying his whole family. But that could have been just an assumption, and either way it wouldn't make much difference to him if it was just his siblings or his parents too, as by that point he would be training away from home. Still, interesting question. South Reach is also ravaged by darkspawn (we hear from its Bann in Origins), so it's possible that his parents died there too. nvm, Owl clarified that. So they did die in Honnleath, and the kids moved away much much older than I'd originally figured.
It's also possible that their deaths weren't related to the darkspawn or the Bligh wasting disease at all, but the civil war, as you mention, and that would make things really interesting for my world state, seeing as Loghain has to stay in Skyhold for a while. Would Cullen resent him for it? Would he even know or comprehend the full extent of the political games the nobility was playing during the Blight? Would he not know the difference and only know that his parents died "during" the Blight and not the direct cause? Hmmmmmm. Lots of headcanon to readjust there.