The AI tends to be not very good at handling unit upgrades; I have a suspicion that until some serious civ-specific AI work is done (not sure how much has been done if any in this regard for Jotnar), the AI would have no clue how to deal with the Jotnar unit mechanic. I can imagine it spamming its little 1/2 Thralls in a panic to compensate for its apparent lack of combat unit options.
You don't have to leave the screen completely, just disable a player slot, then re-enable it for an AI player, and the assignment list will refresh itself.
Does anyone else have experience playing with them as AI?
One potential problem I see, is that the Jotnar AI benefits MASSIVELY from the -75% upgrade costs that they naturally get, because their whole civ is pretty much focused around upgrading. That's pretty unbalancing for an AI jotnar, but I do wonder if they'd just crumble and fail without it.