is it possible to install a program as a start up program using MSI installer?
Yes, that's possible. Here's one way, apparently. And here's another.
Didn't try it myself though. If someone wants a program to appear in startup, they can just place a shortcut in the start up folder (of course, I'm aware that sometimes you have to offer it kindly to your users ;)
You can do a silent install for an msi and script that via batch script or compiled application. Then schedule that script/program however you want. Without AD you might just insert the call to the script in the registry under RunOnce.
Or even better in an AD environment: How to use Windows Installer and Group Policy to deploy the VPModule.msi in an Active Directory domain
Sure, simply use the registry Run keys to start your application. e.g.
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run
There's nothing special about Windows Installer in this case, you could easily use a non-MSI setup program to accomplish the same thing.