Ok so we ran into some trouble when we tried to uninstall cloudlinux from one of our test servers, following the instructions on the cloudlinux website seems to do half the job. We followed the instructions from this blog http://www.linuxspy.info/tag/uninstall-cloudlinux-from-cpanel/ which is a lot more accurate, but still at the end we couldn’t ssh into the server and the cpanel crons stopped running. We solved the ssh problem by opening up /etc/pam.d/sshd and removing the line session required pam_lve.so 500 1 wheel,other, now we where able to ssh but not su !!!!
After many hours of investigating the conclusion was: if you plan on uninstalling cloudlinux you will be left with a busted setup, so it is better to just re install your whole system.