Disable Time Synchronization on Ubuntu

Are you sure ntpdate is your problem? It does not run as a service and usually only gets run when an interfaces is brought up on recent ubuntu systems.

To disable ntpdate on an Ubuntu system without removing it you could simply update /etc/default/ntpdate and add the word exit as the first line or change the NTPSERVERS variable to be empty.

Are you sure the issue isn't related to your VM tools package? Are you sure you haven't actually installed a full ntp daemon?

Intentionally keeping time out of sync in a single VM can be somewhat difficult. The system clock is one of the resources that don't really get virtualized very well.

ubuntu-minimal is the package which provides many other packages in the Ubuntu minimal install. Removing that package does not cause any problems. Later on if you want to get all the packages in a minimal installation then just reinstall ubuntu-minimal.