I saw something like this in 2.4 using the stun rod as well. My personal experience was:
-Research stun rods.
-Read the research report, noticed that it was supposed to be a two handed weapon.
-Made one and fixed a soldier load out for alien capture.
-In battle realized that my soldier could use the stun fire modes with his pistol still in the other hand.
-Tried it, result: "alien was stunned".
-Checked containment after the dropship returned, contents: none.
-Wave hands in the air in furry.
-Try again, see previous three steps.
-Chucked stun rod in storage where it collected dust.
-Thought about it for a while, tired again without anything in the soldier's other hand.
-"alien was stunned"
-Checked containment after the dropship returned, contents: DING! "You've got live alien!"
Maybe the stun rod should have whatever makes rifles, ect, unusable while something is in the other hand?