It can be done, but it's a semi-permanent solution... To enable or disabled the buttons you'd need to reboot.
Since you're already rooted, it's not overly difficult (if you don't mind fiddling with system files)..
Using an app like root explorer Browse to /system/usr/keylayout check the various .kl files until you find the files that have Lines similar to these
key 114 VOLUME_DOWN WAKE
key 115 VOLUME_UP WAKE
These lines are from my nexus 4, the key number may be different, you're looking for the VOLUME_UP and VOLUME_DOWN tags, these are the hardware volume buttons. If you Put a # in the very first character position on the line, that will comment out that line... Save the file, reboot the phone, voila, disabled volume buttons... ( but you'll need an alternate way to modify volumes)
Oh! One more thing, if you want to be able to still get it a updates, make sure you make a backup of the original file(s) so you can revert the changes when there's an available update. (saving any changes to the files breaks the ota updates... Even undoing your edits won't make ota work, you need the original files, checksums, etc to allow ota...)
Make sure you do an nandroid backup before you do this, in case something goes wrong, that way you can restore it and still have a working phone.
I've used this technique to repurpose hardware buttons before.