In version 4.0, you can customize the exact height where the ooze shield stops printing, so if the end of your print only uses a single extruder, you can turn off the ooze shield for that section. To do this, you can use the new Variable Settings Wizard. Go to Tools > Variable Settings Wizard, and enter the height where you want to stop the ooze shield. You can also move slider at the bottom of that window if you want to see this location on the model itself. Once you know the correct location, click "Add Location" and the you can finish the wizard by clicking "Split Process". You will now have 2 processes, one for the bottom of your printer where you want the ooze shield enabled, and another for the top of the print. Double-click on the top process and disable the ooze shield for that process (on the Additions tab).
We found that even after the second extruder was no longer used, you may still want to keep printing the ooze shield for another 10-20 layers to catch any remaining ooze, so this way you can customize the exact location where the ooze shield stops to make sure the shield protects the part until the second extruder is done oozing.