Hmm I suppose that's the limitation of merging Resident Evil gameplay with TFs, you can just lose core items. And that's exact issues popped in the past with keys so I think I made it that they don't get destroyed if I remember correctly.
The combat itself has a rework planned with better aiming, and new items (ex. fire extinguisher that has charges and just stuns enemies) or indications that you hit them etc. so probably a long term solution will be delayed until then, but I think you are right.
I'll look into adding gun into excluded items list so it doesn't get destroyed or maybe also make it respawn, that should be helpful for time being. Good call.