Steps to reproduce:
1) Create a profile. Select one or more options to create a uf_join record (i.e., "User Registration")
2) Edit the profile. Uncheck the "Active?" checkbox.
3) Check contents of civicrm_uf_join table. Entries still exist for the uf_group_id of the disabled profile, and are set is_active=1 , which is potentially misleading.
Note that the problem does NOT occur if the profile is disabled via the "Disable" link on the overview page.
The bug is contained in CRM/UF/Form/Group.php
Patch against 2.0.5 is attached.
An improved workflow would warn the user that join entries are being deleted, and ask for confirmation, just like the working 'Disable' link does now, but this patch solves the immediate problem.