Speaking for MOO 1, which is primarily what i play: I take it if it's convenient, but it's low priority. The multiple free techs are a great hail mary for clawing back into it against a runaway AI! But generally I find I win or lose games long before my fleet is advanced enough to waste the guardian without making a specific anti-guardian fleet. (bajillions of NPG fighters, that sort of thing)
I primarily play on average size/impossible, and that probably plays a role in the decision. The guardian is wimpier on lesser difficulties, and larger galaxies often lead to longer games where higher tech levels are achieved and fleets are larger. When you can end an average size game with Megabolt cannons, who needs death rays?