I assume you are not using a QV Server, so you store your qvw files on a share and currently everybody can access them, right?
So you could use file based security (similar to what the QV server / publisher does) by setting appropriate access rights to the files / folders.
And as you already know, you could use section access to also control the access from within QV, i.e. QV will ask for credentials when opening the document, either by passing Windows credentials or via a dialog box.
Check this for an introduction to section access, it also covers the Windows authentication via NTNAME and NTDOMAINSID. Please take a look at the samples, too.
The document covers also how to perform initial data reduction based on section access, i.e. limit the visible data per user.
Hope this helps,