That is a good point, and I agree that scripts can be ridiculous. I was rather think there was extended footage that I haven't seen. (I haven't gotten the DVD yet.)
In any case, what else explains Sidious being disarmed? Unlike the AOTC script saying Dooku is crap (Which is clearly an exaggeration on the part of the script) Sidious went from having a lightsaber to... not having one.