It's still very likely that Aku could have beaten the Guardian if he'd encountered him. Everyone seems to forget that we have no evidence whatsoever that the Guardian possesses any weapon or power which can actually harm Aku. The Guardian is ridiculously, absurdly strong and durable.
The issue with Aku, really, is that he'll take no harm from, or easily regenerate from, any wounds inflicted by the vast majority of the weapons in the Universe. We have no evidence that the Guardian, powerful as he is, has (can materialize) any weapon "forged from righteousness" like Jack's sword, which can actually hurt Aku without him regenerating. Sure, the Guardian was able to whip out a big sword that didn't break against Jack's sword, but that's no evidence it was an allmighty magic-sword--It could have just used some kind of really hard metal like the stuff the Ultra Robots were made from. That's far more likely, really, given we've seen the Guardian exhibit no evidence of any kind of supernatural weaponry. So yeah, no matter how strong the Guardian is, he most likely couldn't hurt Aku.
So, if Aku found the time portal? Probably grew to one of his Mountain Sized forms and just wore out the Guardian's seemingly-limitless stamina until finally squashing him.
So the question is, did Aku find that portal? Jack seems to think he destroyed "all" the portals, so. . . . .probably?