I have had to pen mine up due to predators, and they do get used to it. I think they still produce healthy eggs. They get outside, get fresh air, and any bug that goes in the coop/run. Unless you cannot create a run, making a run/coup and keeping your birds in it 24/7 won't be that big of deal after a week. Chickens get used to things, but hate change.
summer is coming and you could go out for a bit in the evening with a long stick, and keep them on your side if you wanted to. However, at first, don't let them out. Pretty soon 'out' will be strange and they will be a bit uncomfortable there.
I have found the more you let them out, the farther they range.