With the "Manage Conflicting Processes" feature, you can close, well, conflicting processes.
It would be nice if there was an option feature, allowing customers to configure the relaunch of closed apps once the installation is done.
This would be nice because the installation is done as SYSTEM, so if customers were to use a custom post-install script, they would need to launch the process for the logged on user.
It would be nice if a feature similar to the "Execute-ProcessAsUser" from the PSADT would exist in the Publisher / SaaS