As you probably already know, making requests to the workers to keep the dust down is a pretty fruitless task. They will nod and say, "Yes, yes," but not much will be done about it. Honestly, this is no knock on the installers. Most are completely well-meaning, but they just don't understand the gap between their tolerance level and the tolerance level of some homeowners.
Even though window replacement is a fairly clean project, judging from the way you describe your reaction to dust I would say that you will be bothered by it. It's mainly removal of the old windows that will bother you. I've rarely seen such that all of the windows are clean removals. At least one or two window will entail a good amount of chopping and pounding (especially if they are really old windows). They will need to use a reciprocating saw, too, which creates sawdust.
Certainly nothing as insidious as drywall dust. But you may want to stay at a friend's house while they do this, and invest in a maid service to clean up the dust afterwards.
