This technically can be done in various ways relating to InstallShield, Wise, WiX, NSIS or other installer platforms, but generally speaking is the same concept all throughout whether you are using third party tools or creating your own bootstrap/windows installer project/custom action.

An MSI file contains tables of data. Within these tables, there is one labeled “property” which contains a series of string/value items. The properties which control visibility of repair/modify in button are referred to as:

ARPNOMODIFY
ARPNOREPAIR

In order to modify the MSI tables and change these properties you must first be able to modify the MSI file. This can be done one of two ways:

Option 1:
Download and install the Windows SDK Components for Windows Installer Developers.

Once downloaded and installed, navigate to “\Program Files\Microsoft SDKs\Windows\v7.0\Bin” and run “Orca.msi” to begin the install for orca.

Once installed, run orca and open the propery table and add an entry for ARPNOREPAIR and set its value to 1.

Option 2:

As an alternative, unless you have some other reason for DLing the SDK, you can totally bypass the 2.5GB DL just for a little orca file by using an awesome proprietary tool called SuperOrca :).

SuperOrca IMO is much improved over the basic MS orca, but the end result is the same. Open the MSI, navigate to PROPERTY table, and add the entry with a value of 1, save, test.

For C++ or custom action programmers, you can call MsiSetProperty and pass in ARNOREPAIR for the name and 1 for the value for the same end result.

MsiSetProperty and MsiGetProperty cannot be called from your typical C# installer class/bootstrap DLL, since the handle to the installer is never passed in.

For a little background history, in my particular case, a custom action in the installer is targeting a DLL I created (separate project in the same solution). This DLL inherits the installer class and overrides the install and uninstall methods.

References
Stackoverflow, http://stackoverflow.com/questions/819722/remove-repair-option-screen-from-msi-installer
MSDN (ARPNOMODIFY), http://msdn.microsoft.com/en-us/library/aa367590%28VS.85%29.aspx
MSDN (ARPNOREPAIR), http://msdn.microsoft.com/en-us/library/aa367592%28VS.85%29.aspx
MSDN (Windows Installer SDK), http://msdn.microsoft.com/en-us/library/aa370834%28v=vs.85%29.aspx
ureader.com, http://www.ureader.com/msg/16531570.aspx
Orca, http://msdn.microsoft.com/en-us/library/aa370557%28v=vs.85%29.aspx
SuperOrca (Pantaray), http://www.pantaray.com/msi_super_orca.html
MSDN (msisetproperty), http://msdn.microsoft.com/en-us/library/aa370391%28v=VS.85%29.aspx
MSDN Blogs (msisetproperty,getproperty), http://social.msdn.microsoft.com/Forums/en/winformssetup/thread/e7726f09-79eb-4fe1-ba2b-add79514f5f5
MSDN (create a custom action), http://msdn.microsoft.com/en-us/library/d9k65z2d%28v=vs.80%29.aspx