That is correct. It locks the front door, but let's existing leads continue through the flow. If you want them ejected out, just run a single flow action "Remove from Flow" on the members of that Smart Campaign.
Jennifer, when you deactivate a trigger email campaign it stops triggering on new records, but continues to run for existing records. To deactivate for existing records, you should go to the list of campaign members, and under list actions select "remove from flow" then choose the campaign you just deactivated.