Guardians do not come in with waves. You pissed him off by sending the transports in, which freed up the guardian and maybe some other ships with it in one of those systems. This is why when scouting that early in the game I send the scouts in by themselves with nothing else at all, because other stuff tends to make the AI angry, and then it tries to kill you. Yeah, it's harder to get your scouts through, but that's what sending them in groups is for, or unlocking mk2 if you need them. Post a mk1 scout on at least each planet bordering you so you can keep an eye on anything threatening you, and then take all the rest of them left over and push them through as a big group, but loose, not in transports, and that should be enough to make it at least a few systems away in any direction even with the them getting decloaked, especially if you don't mind flying them around manually now and then. Still going to need mk2 scouts fairly early that way, though, but they're cheap enough, and you get a lot.
That's a hilariously awesome way to lose, though. What could possibly go wrong that early in the game? Heh.