Would the right way to handle such files be to use the FUSE filesystem (when it's done) to hide them from apps?
On the one hand it sidesteps the problem, but as a recent blog post by Microsoft's Raymond Chen http://blogs.msdn.com/oldnewthing/archive/2008/04/14/8389268.aspx shows, it IS possible to get into this kind of problem in Windows too.
--- Chris