Personally, I think fixing this and other weapons related bugs should be priority 1 for the dev team, because once these issues are fixed, the beta will at least be playable at all.
NOW one can play through a max of two or three scenarios before one of these bugs kick in and one is forced to start a new game.
The fact that alien weapons are not usable until researched however is okay IMO. But the they should probably not be displayed in the equipment screen or the equipment buying screen to avoid confusion.