Could we use SLPS to provide licensing to this .msi package created using Installshield?
SLPS can be used. To do this requires some pre-steps to the .msi being created. What you would do is use SLPS with your .NET .exe's and .dll's to create the licensing environment you want for your application. This processing will generate a couple more .dll's. You would then re-create your .msi using InstallShield.