When rebel players choose to do an Agenda side mission instead of the 2 rebel side missions that are in play, does the Agenda mission get recorded in the next side mission slot of the campaign log, thereby stealing the rebel side mission slot?

Yes. Unless the agenda mission says it is a "Forced" mission, then it would go in the "Forced Mission" section.

Wait, does that mean if it is a Forced Mission, the Rebels still get to do another Side Mission afterwards?

I thought Forced Missions occupied a Side Mission slot on the Campaign.

Nope, Forced Missions get written in the Forced Mission section of the log (you can create extra slots if you need more than 4, there's no limit except in available influence). They're done at the threat of the current mission slot (or the last mission completed, I'm not sure on this).

But these are specifically Forced Agenda Missions. Agendas also have Side Missions (First time I played Imperial Player I didn't realize there were two types of Agenda Missions). The Side Missions replace a side mission slot. They're the ones that are optional, but if the rebels go off to another side mission, the imperial player immediately removes the agenda mission and gets the reward. Forced Missions can't be avoided, but don't replace other side mission slots.

Forced missions, whether from a Side Mission or from the Main Mission are played immediately at the same threat level of the previous mission.

Hypothetically, after the Imp wins Aftermath and plays a forced mission, that mission would activate, and since the last mission played was at 2 threat, the threat level for the forced mission would be 2. When the mission is completed, you continue on path on the back of the book which would be a side mission, which is what you are supposed to play after Aftermath, and the heroes will choose one side mission to play.

Hoped that helped

Wait, does that mean if it is a Forced Mission, the Rebels still get to do another Side Mission afterwards?

I thought Forced Missions occupied a Side Mission slot on the Campaign.

You may already know this, but there are also rules regarding upgrade stages associated with forced missions that differ from the standard missions. These are explained in the RRG.