Hi Jason, if you have someone in a wait step and you deactivate the program, they will not be removed, and will continue to go through all remaining flow steps. By the same token, if you have someone in a flow step and you change the length of the flow step, they will exit the flow step when they initially were scheduled to exit -- not your new timing. Any new leads that enter the wait step will be on the new timing.
To stop that email from going out, you'd want to run a flow step against anyone in the program to "Remove from Flow".
One additional thing that I recently learned about flow steps that seems more backward to me, is that if your wait step is the 2nd item in your flow, and you add anything between steps 1 and 2, the wait is now step #3, and upon exiting their current wait step people will go into another wait step.
These are all very important to keep in mind when launching or changing programs!