If you are deploying your MSI packages via Group Policy in AD, it will allow users to install managed applications with elevated privileges (higher than admin privilege).
This privilege can also be set on individual workstation using gpedit.
I would suggest you begin by looking at the pages in msi.chm called "machine policies" and "user policies" for a key you can set called AlwaysInstallElevated
If running MSI's with elevated privledges does not meet you Security Guidelines you will have to deal with unsecureing directories and Files. The LockPermissions table houses all of the entries you will need. If you take this approach I would suggest getting yourself a copy of FILEMON and REGMON so you can see what files are being accessed during application preload.