Unable to uninstall the Field Collection module
I guess you solved this already, but if somebody else stumbels over this, here my 5 cent on how to get rid of field collection. I encountered the same issue as @nitnac23 and was only able to get it out via direct data base manipulation:

definitely make a DB backup this time (might save your website)
Remove all field collection fields from your entities
run the cron potentially multiple times (this cleanes up the entities - fingers_crossed)
it is important, that you no longer have fields pending deletion as a reason for not beeing able to dissable fields collection (under /admin/modules/uninstall/) - if you still have it, try running the cron again (more infos here)
clear the contents of the database tables field_collection_item and field_collection_item_revision directly in the database
uninstall field collections now via /admin/modules/uninstall/
if you have still field_deleted_* tables in your DB, drop them (I had 12 before runing the cron and still 2 after unsintsalling the module)

That should do it hopefully :)