You should be using the register_deactivation_hook and/or register_uninstall_hooks. That may be why some functions don’t work. I’d have to do some testing to be sure, but loading your method directly like WP_Plugin_Janitor::cleanup( $opt, $cpt, $tax ); seems like a pretty good way to skip over some of the WordPress load sequence or to run things out of order.
As far as loading the class twice, I have an answer, but that is a different question and not really WordPress specific. 🙂
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