If your customers use SMS, then you are in a clear ... SMS supports EXE. You enter the command line when creating the "Program", and clients probably already call msiexec to start MSI. I'm also sure that SMS precedes the MSI file :)
However, if they use Active Directory / Group Policy Objects.. then you are SOL, because it depends on the MSI format for deployment.
If you want to stick with InstallAnywhere, there are many MSI repackaging tools available. Assuming you are looking at the main application (device drivers may be a problem), then repackaging should be a pretty painless process.
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