I play Alpha Strike, choose my 3 Might unit, and target three enemy 1 Might Recruits. My opponent reacts with Stupefy on my 3 Might unit and En Garde on one of their Recruits. After all spells resolve, can I choose to kill only the Recruit that is now 2 Might?

No. When ceasing to be a target under 355.14.h., you cannot remove an arbitrary number of targets—you remove only enough so that the number of targets matches the damage being split (do as much as you can). If only En Garde had been played (no Stupefy), you could not kill the 2 Might unit either.