Would they have taken part in the time war?
It isn't clear. We know that the Eternals and various other immortal/transcendental beings fled the universe during the Last Great Time War, although I don't think the Guardians are ever mentioned, and they could have always come back when the Doctor ended the War. (See Doctor Who Annual 2006.) So far, they haven't been mentioned in the new series, the New Series Adventures novels, the Big Finish and other audios that have been produced since the new series started, etc., so we really don't know.