5 years experiences in customizing/repackaging of software installation.
Customize MSI installation/uninstallation action is my work, To solve your problem, I will
1. Add an custom action to check if the app is running
2a. If No, nothing to do & uninstall the MSI
2b. If Yes, popup a message box asks user to close the app. By closing the message box, uninstallation will terminate
BR,