Guys, I really don't want to come off as unwelcoming to your ideas, I am actually desperate for them, but while I can't speak for the whole team, I cannot suspend my disbelief that high. Aliens have different minds, sure, but they interact with the same outside world that we do, and tools in their hands must work the same ass in our hands. Especially tools with a purpose as primal as killing.
I was thinking about some sort of a psionic lock on alien weapons (note how they don't have scopes!), but it's of no use - the actual mechanism is purely physical, so our scientists would easily circumvent any safety guards given enough time. Which is exactly what happens in vanilla, I think.
And by the way: the problem isn't that alien weapons are too powerful in X-Com hands; the problem is that you get them too soon, which invalidates almost all other weapons so you don't have the time to enjoy them.
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Now, regarding my test campaign. I decided to become a little more forthcoming to the players and move the getOneFree feature with key techs to Leaders and Commanders as well. The reason is, Engineers are a bit too easy to come by in enough quantities, and even if you catch one, it'll likely result ion something useless, like some UFO information. Since Leaders and Commanders must come from somewhere, I assume they may have some engineering and medical knowledge, so now they also yield this information (but not the standard UFO/alien race info).
In May, I encountered a Large Scout with Ethereals (playing on Veteran). Man, this was unbelievably hard with no sci-fi weapons; I certainly wouldn't have managed without save scumming. I somehow managed with explosives, a flamer and a minigun, but man. Still, I kinda like this balance, after all you don't have to win, or even attempt, every mission.
I also increased Tank/Cannon's damage, because it was next to useless. It's still nothing awesome, but at least it has a chance to kill a mid-tier alien now. Update in the attachment (also new sounds etc.).