Firstly, he never expect that the battle will turn against him cos Itachi is also an edo before he break it. I believe if nagato knew that, he will have to a way to counter the amaterasu and moreover nagato was sealed because he was already weak after bee, naruto and itachi counter is technique.. Moreover it also part of kabuto plan..not forgetting that nagato had to regenerate against itachi.
when itachi used amerterasu