I don't know of any available way that will stop Windows Installer from Self Repairing MSI packages.
Self repair is one of the most powerful features of Windows Installer. It gives the installation the ability to monitor and heal a broken MSI Package automatically.
I am not sure why you want to suppress the self repair feature. Here are some common causes of self repair.
When an application's detects that a component key path is missing, the installation initiates self-repair.
Your installation might self repair if it contains HKEY_CURRENT_USER keys and has a component key path of an HKCU registry key. Self repair occurs the first time a new user logs on and launches the application. Windows Installer depends on the self repair functionality to distribute the HKCU keys to other users on the machine who are using the application.
Also when Windows Installer checks the registry key paths of the components, it verifies that the key exists, and that it has the same value that was specified in the .MSI file. If your application modifies the registry key, it can cause self repair to be triggered.
You can use Event Viewer to diagnose why your package is performing self repair. Event Viewer is available on Windows XP, Windows 2000, and NT.
Also you can use MSISPY to find out what components in an MSI package are causing self repair to happen. This utility is part of MSI SDK.