I never used pecl... but seems that
Code:
pecl uninstall apc
aptitude purge php-apc
aptitude install php-apc
should do the trick... make sure you don't have any lingering references to apc in the main php.ini, and edit /etc/php5/<type>/conf.d/apc.ini to set your sizes.
All this assuming you can live with a bit of downtime in case of something going bad. >.>;
Good luck!
PS. The reinstall of the repo version with aptitude might be actually unnecessary... but it's a way to start from hopefully-clean state.