I've successfully run InSpectres for two before, but that was as more of a demo than a running campaign. An established franchise which needs 20 or 30 dice worth of successes for its average mission might be a little tough for two characters to pull off on their own. Here are some things to consider.
Multiple confessionals. Sure, why not? Give them an extra one apiece. Inspectres is a reality TV show game, and in a reality show with a smaller cast, each member can have multiple aside spots per episode. That just makes sense.
"And their dog!" If you have two players, they should both be playing normal agents. Weird agents can succeed on skill rolls and help other agents out, but their successes never rack up Franchise Dice for the mission. However, this also means that if you have two players, they can create and share custody of a Weird agent without getting any additional benefit toward racking up Franchise Dice for the mission.
Troupe play. At some point, somebody's going to need to recover for long enough that they'll be out of action for a while. At this point, or even before, it's fine to just create a "new character" and keep on going, and pick who you're going to play at the start of the session or maybe when the call comes in. The only mechanical difference between "new characters" and veterans is their Cool score, which is fairly volatile anyway.