It is nothing unique to non-law enforcement involved shootings. The firearm can, and should, be taken as part of the proper course of a shooting investigation. Firearms involved in law enforcement shootings are taken from the officers just as they are from regular citizens. The difference is after each shooting, I have had a replacement firearm given to me almost immediately to be sent home with. Nevermind I had a small arsenal at home anyway.
As has been stated, shooting investigations are very thorough. Even when an involved party is telling the exact truth as they see it, events unfold differently to everyone and even truthful statements can be shown to be in error. The mind does not work the same way under the stress of a shooting and what a shooter swears to be the case is often not the case. On point, people often think they fired a few rounds and in fact fired several. They think they were standing on one side of a barrier when in fact they were standing on the other. The variables are endless.
The handgun is taken, number of rounds reported as being fired compared with the shells on the ground (if applicable), the number or rounds left in the firearm, etc. Bullets, or fragments thereof, are extracted from the subjects body. The firearm is test fired and the bullet markings compared, etc. This is especially important if more than one person fired where it is important to deem accountability and responsibility for each shot fired.
Truthfully, you should not be offended if a firearm is taken after a shooting incident. You should be offended if it is not because that investigation wouldn't be very thorough and may play against you.