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So if your running from inside inventor as an add-in then this must happen before you code even gets a chance to load:
Inventor startup, Inventor add-in load. You can't stop those processes with your add-in level coding. You can tell the most all of add-ins to NOT LOAD by user settings, then have the add-in manually load all the add-ins that are supposed to be there.
Being an add-in locked into a single (apartment) inside of a single instance of Inventor, you are limited to multi-tasking options, I get it.
You can make a standalone exe using VB.Net and WPF window (if only 1 button to activate), that then runs all your code. This compared to your existing add-in should be easy by changing your VS project from class library to application with the Application tab of your project properties (Application type dropdown). This would require you to designate a main window as a startup window. (project templates create MainWindow.xaml, but you can use any window file). IMO it is easer to use a standalone exe than the add-in because it tends to be version independent.
Other option would be to have a simple exe app call your existing add-in, after managing the inventor startup/cleanup process from outside of inventor. I can't help but to think you are reinventing the task scheduler that inventor comes with.