Other than just creating a separate template for each section, one way you could do it is use a Template Variable to assign the stylesheet to use for a particular document.
For instance, you could create a Template Variable called MyStylesheet and assign it a DropDown List Menu as the Display Type. From there you could assign Input Option Values as "style1.css==1||style2.css==2" or the like where style1.css or style2.css are the names of the stylesheets stored on the server. The Default Value of the TV could be set to 1 or 2 depending on how you assign the values in the Input Option Values box. Then you just assign Template Access rights to whatever template you want to control this TV with.
Now you can insert in the TV into your template. The code could look something like this:
<style type="text/css">
@import url('/assets/site/[*MyStylesheet*]');
</style>
The result would be that whatever stylesheet you choose for the TV in a document assigned to this would show up. The drawback is that you would have to make sure that you choose the correct stylesheet for every document you create using this template.
A more advanced way to doing this without having to assign a TV would be to create a snippet that detects which folder a document is in and assign the correct stylesheet. Basically, you would have a unique document ID for Folder1 and Folder2. A snippet could be written that would basically output the name of the stylesheet to use based on whether the current document equals a certain document ID or if the document is a child of a specific document ID. I’ll see if I can write up a quick example for ya...pretty simple really.