Hi,
I assume that the requirement entails using some sort of remote distribution system, and thus will not involve running the user interface.
That said, this limits your options to using a Major Upgrade to accomplish this. You'd basically add a Major Upgrade item in a new project and set it up to remove the other package. To avoid registering the new package on the system, you could just condition out the actions at the end of the Execute sequence that begin with 'Register' or 'Publish'.
But, I suspect there may a better way of handling this with your environment. What method are you using to distribute the installation?