They should get paid more for the additional mess.

Usually one finds it difficult or nearly impossible to find a great housekeeper. Unless you want to lose her, pay her the regular amount because the rest of the house is cluttered with boxed items from the kitchen, the temporary kitchen set up in the dining room or laundry, and the homeowners are more grumpy than normal! You are going to be under stress and will appreciate the clean sanctuary.

I agree with the others.

I'd definitely keep paying them the same amount! I'm guessing they usually allot a certain approximate amount of time to clean your home; if they find they are finishing the job more quickly because they aren't cleaning the kitchen, you could suggest they find something to deep clean that isn't part of their usual routine(e.g scrub the shower grout, clean the windows, launder window coverings, etc). Or send them home early and be grateful you have a great cleaner!