It is pretty common the first time the chicks are in pure dark for them to freak out, say they are moved from a brooder to the coop. But they soon get over it and go to sleep, say 5 to 15 minutes. The second time it happens they are a lot less concerned. Very soon that is just the way it is...
How long did they complain loudly? Chickens often don't like change but they are also typically pretty adaptable. I anticipate if you are consistent they will quickly get over it.
I agree with the others. A broody hen does not provide any lights under her when the chicks sleep under her. Your plan for light during the daytime and dark at night is good.