When deploying software the best way to edit the MSI (remove shortcuts/disable auto update features) is to do it is through a tool called Orca.
Orca is a Microsoft created tool that reaches into a MSI and changes settings inside it without having to repackage the MSI using other tools (e.g. WinInstallLE), the advantage of this method is you have a cleaner software install where repacking sometimes allows mistakes to creep in (e.g. random reg entry changes). Having said that some MSIs get poorly created by the software developers and so don’t allow this modification in the first place.
Either way Orca is a tricky tool to get installed and so the screen shot sequence below shows my way of getting it on your PC.
Before you go any further you will need this link – http://www.microsoft.com/en-gb/download/details.aspx?id=8442