Goku doesn't have any defense against being Taken, so theoretically Oryx could just do that right off the bat- but let's just assume, for the sake of argument, that Ki is roughly equivalent to Light and thus he'd be immune. Then, it really depends if when you say "the entire Destiny Universe" whether you mean all the various forces are simply fighting alongside each other, or are able to work together and strategically conflate their abilities. For the former, I'd say Goku would win. He might have some difficulty with higher level Hive, particularly the Deathsingers, as well as some powerful Vex, like the Gorgons and Atheon, but I think just about everything else he'd kamehameha out of existence. Now, if it's the latter, Goku would loose. Like, a lot. If the Taken hijack the Vex and that final end state of the Universe where everything is just trillions of Taken Vex worlds (you know, the thing that the Vex needed the fate-defying abilities of the Guardians to avoid,) then Goku would stand a chance.