Based on my understanding, you would not need to execute OnNavigatedTo/From methods if you would not be navigating to a particular View.
Anyway, if you may need to execute the OnNavigatedFrom() implementation before removing the View from the ItemsControl, you could manually invoke it right before manually removing the View.
You could pass null to the NavigationContext argument if you would not need it, which I believe you don't, or you could manually create it otherwise. The solution would be as follows:
INavigationAware viewModel = viewToRemove.DataContext;
viewModel.OnNavigatedFrom(null);
IRegion myRegion = _regionManager.Regions["MyRegion"];
myRegion.Remove(viewToRemove);
I hope this helped you.