Think about it:
1. Matt and Jimmy are good friends. In the very first StarCraft campaign, you find Jim in the second, if not first mission (excluding the tutorial mission). Wouldn't the former magistrate and Jim be friends after being together for so long?
2. The former confederate magistrate was a commander of sorts, Matt's a commander of sorts...
3. (POSSIBLE SPOILER, I'll assume you played the entire campaign for this one) Ignore the whole Matt Horner thing for a moment and go back to SC1. Now go up to the part where Jimmy and his newly formed Raiders group hijacks the Hyperion (this is right after the last mission). Who do you think Jim would leave in charge of the Hyperion? The former magistrate, who else? Now assume that the same former magistrate never died, and he still commands the Hyperion in SC2...
Personally, I think Matt Horner = former confederate magistrate (same exact one from SC1).
P.S. I know the SC1 campaign because of this, which you could play the moment you get it set up:
It's apparently fine tuned often, so it can only get better. And yes, all 6 campaigns, from Rebel Yell to the end of Brood War, is all available.
Oh, and here's how you could set it up (but its a bit outdated):