I was looking at that a while ago. The drawback is that you would have to keep a copy of the installation files on the local drive in order for the MSI to uninstall properly.
You can:
1. In the MSI, have two scripts and all the installation files for the app.
1a. Script 1 - condition set to Not Installed, calls a script which uses for LaunchAppAndWait function to SETUP.EXE for installation.
1b. Script2 - condition set to Installed, calls a script which also uses LaunchAppAndWait to call SETUP.EXE for removal.
Of course, you will have two entries in the control panel for the application - one for the MSI, and the other for the SETUP.EXE based install.