I think it was established by FL some years back, that Xenomorphs and other monsters are not NPC; monsters are not "characters". That said, my memory is awful so I could be mistaken.
When I started GMing Alien RPG, I allowed my players to pin xenos, and thereby set a unfortunate precedent in our games. I have regretted it mightily, as it weakens the xenos greatly, thereby diluting the horror aspect of the game; with a single (extra) success using their pulse rifles, each CM player can halve an alien's effectiveness, and therefore scariness.
The solution in my game, having established the mistake (and we're too stubborn to change), is to rule that while I continue to allow pinning of your garden variety xenomorph, I do not allow it for bigger and badder variants, like chargers and praetorians and queens, etc. That helps a bit, and it actually makes the bigger variants even nastier, comparatively speaking.
*shrug*
If you have a choice as a GM, without upsetting the players or whatever, then don't allow PCs to pin xenomorphs. That's my advice, at least.