First, How do you check the version of Xenonauts you have from Desura? Whatever I have, it is the latest I am able to upload as of 26 Dec 2012 so I guess it is v8.5.
When in combat, I used all my missiles so I placed the handgun in the hands of the soldier. The missile launcher was automatically placed in the backpack, but the weapon was now armed. I was able to replace the handgun with the launcher and shoot.