I'd suggest a set of defaults that would apply to both sides, based on relative threat as well as unit abilities. On the AI side this could be varied by a random 'commander demeanour' factor, from cautious to gung ho. The AI may also be influenced by any overall stance or goal prioritisation at that time, e.g. prepared to take higher risks to push through a high-priority objective. There could also be a surprise factor that should give some sort of bonus to the unit less affected, e.g. on a 'hunt' move.
I envisage that a 'react' would be pretty much the same set of behaviours you'd expect the AI to carry out during the command phase. I'm not necessarily talking about any new functionality - I'm suggesting that it would be a trigger to standard game functions, and would relate to dealing with a threat. For example, a scout team encountering a tank would retreat immediately rather than fight, whereas a deployed ATGM team would fire a shot and then relocate ASAP. MBTs would go toe-to-toe as usual. In some ways this would be the same as if the encounter happened during the last second of the WeGo minute - the AI would then have to make similar decisions based on this new information.
Perhaps some new features could apply; the human side could allow setting a 'retreat to' location (based on current waypoint) while the AI would have to determine where's the nearest cover at the moment of encounter. That way an ATGM team could sit tight until a target appears, take the shot, and then scarper to that predetermined location.
I put a post in to the suggestions/requests thread along these lines.