There isn't a way to simply disable the indexing part. It's an all or nothing service. The description of the WSearch service states:
"Provides content indexing and property caching for file, email and other content (via extensibility APIs). The service responds to file and email notifications to index modified content. If the service is stopped or disabled, the Explorer will not be able to display virtual folder views of items, and search in the Explorer will fall back to item-by-item slow search."
However, you might be able to control it through drive/folder properties ... from Explorer, you can switch it of for an individual drive (see the properties of a drive; there's an option "allow indexing service..."), or for a folder (folder properties -> advanced -> "For fast searching, allow indexing service...").
EDIT ... a bit of googling, and the above properties are available - if you look at the MSDN page for System.IO.FileAttributes, there's a property NotContentIndexed
with the description The file will not be indexed by the operating system's content indexing service. I would assume that you should be able to set this on individual folders. I don't know if this works if set at the drive level (without a recursive run through the drive), but hopefully it'll give you a head-start on whatever you're ultimately trying to achieve.