How can I disable root on a modded device?
If you install SuperUser you can control which apps are allowed root access.  By default it blocks all requests and asks you what you want to do.  You can give an app access indefinitely and revoke it at any time, or allow only specific requests with a timeout.  Most rooted ROMs come with it pre-installed, including CyanogenMOD, and many rooting methods will install it for you as well.

As an alternative, you could remove the su binary and Busybox from your device to effectively un-root it.