I had the same problem when I carried 1911s. I carried my 1911s in condition 1, but while at home, when I retired my 1911 to bedside duty, I would clear the chamber and load a loaded magazine, but not re-chamber a round. Just my choice, but I didn't like to have a loaded (hot chamber) pistol laying out in the open.
I found that if I took an empty magazine, loaded one round into it, inserted it into my 1911, then eased the slide down to chambered that one round,(making sure that the 1911 went into full battery), I lessened the chance of bullet setback. The 1911's loading cycle is rather violent to the round. The nose of the round hits the frame ramp, then it is forced up toward the chamber. The nose then banks off of the roof of the chamber as it gets forced into the chamber. I believe that It is called the controlled feed principle. Lightly Polishing the feed ramps can help. Choosing ammo that has a bullet with a ball-like ogive can also help. I have had good experiences with GI feed lip (old Colt & checkmate mags) magazines and some HP ammunitions.
As far as shooting 45acp rounds that have been set back, I have done it several times with no ill effects, but I don't recomend anyone else to do it. I have been told be a few seasoned shooters that the 45acp is a low pressure cartridge and it would not hurt the pistol. Other high pressure cartridges (9mm, 40, 357sig etc) are a different matter. I have read that for every one tenth of an inch the bullet is seated deeper in the cartridge case, there is a 10,000psi pressure increase. I have 40cal and 357sig rounds that have been severely set back, and I won't even think about shooting them. I have seen them shot on the police range and no one was blown up, but I still won't chance it.
I agree with the gentleman that stated using a inertia bullet puller would be most effective. I have a friend that carries a 1911. When he buys his defense ammo, he takes every round and runs it through his press to put an aggressive crimp on the rounds to keep them from setting back as quickly. He says that it helps, but it is only hinders set back, it doesn't stop it.