Comment 5 for bug 493852

No it can't. The goal of popularity-contest not only collect what packages are installed, but also determine what packages were recently used. In order to do so, It checks what files are currently open and scans last access time for files belonging to installed packages.

Probably, you may ask an option to disable collection of usage statistics, but it probably makes popcon results less usable. Such request should be forwarded to upstream developers in debain BTS, I think.