Well, one of the guns was a total prop and would have been used for instances when the actor was just practicing blocking and stage business, that would be the rubber/plastic gun. It would not look real in the scene. The second gun would have looked real but it was unable to be fired (should have been the choice here).
That last gun was the "coolest" gun because it was a vintage Colt .45 and therefore felt and behaved like a real gun - because it was. Lots of people would appreciate the chance to handle one (and shoot it properly). Alec felt more "in character" in the shot - and if everyone thought it contained blanks, then they were shooting film (the Sheriff said there was some film from the set that morning, so they weren't just rehearsing.
Armorer is not mentioned as being on set for that shot...which was a huge mistake (obviously, she wasn't a professional or real armorer, just someone with the titlle, IMO. Nick Cage has spoken out about her lack of experience and professionalism in the only other film where she was an armorer.
And then of course, there's the impetuous and apparently arrogant Assistant Director (MOO).
At any rate, there's a fine line between a rehearsal where the gaffer and the camera crew is there - and practice shots. The gaffer, Serge Svetnoy has posted about the situation and provided a picture on Facebook. It is the last picture of Halyna alive. It looks like the set has been cleared of all but essential personnel and if it is a rehearsal, From my POV, Halyna is using the camera in that shot...which is of Alec and a little boy who is playing the role of his grandson.
It's interesting that no one has mentioned that there were also child actors on the set.