In our organization, we solved the problem of Updates by having two release folders say EXE_A and EXE_B. We also have a release folder called EXE which only has links ALL of which points to either to EXE_A or EXE_B from which the user runs the applications.
When we publish a new version of the program, we publish it to the folder that is not referenced in the links and then update the links (EXE). In this way, you do not get into exceptions that users are holding the application / assemblies. Also if a user wants to run the updated version, all he need to do is close / re-execute the link in EXE folder.
