This looks to me like one of those things that often happen during the design phase of any program, missing a requirement simply because it never occurred to the designers that it might be needed. What is needed is an option in the govern -> ships -> going ... -> should go to column that assigns no goto target to the ships selected in the "going to" column. The same is true for govern -> ships -> of type.

Without this, the only way to turn off the autopilot of all ships is to select them one at a time and right click on the ship (which unassigns the ships destination) or select a new target destination by right clicking the mouse on another tile. If you only have a few ships you want to do this with it isn't too bad, but if you have a lot of them it can become next to impossible and extremely tedious (not fun).