Dirk,
The short answer is no. Our programmer looked over the code, and thought there were better things to do with his time. However, the surface reflectance land product MOD09 & MYD09- GA have this methodology implemented in their flags (1 km cloud mask), and you can couple this product with the GQ (250m bands 1 and 2) product and work out something better than the thresholding used in l2gen. The threshold cloud mask has got be one of the biggest problems for us coastal Hi-RES users, as the most turbid days are flagged as clouds.
You should check out, (Doxaran et al. 2009). He has a link to the pdf on his website.
http://www.obs-vlfr.fr/LOV/OMT/fichiers_PDF/Doxaran_et_al_ECSS_2009.pdfCheers,
Anthony