I am kind of confused by your post, do you mean that every time that one side goes down (due to bake backups) they will eventually shut down the other side? Or only if they need to evac guests on the other side?
Correct. For two reasons:
One, it's bad show to be sending more Guests through the ride with the lights on than is necessary. (Often they'll even wait until the other side has cycled out to turn the lights on)
The other and more-important reason is that it's not safe to send Cast members out into the structure with rockets still operating. The tracks intertwine with each other, and to access some parts of the ride, it may be necessary to walk past the opposite-side's track.
So, they cycle out the non-E-stopped side and then set it up to a point where it can simply be re-started. Then they work to reset the other side, evac-ing Guests if necessary. (Though that's rare)
As for those who mentioned about being nervous about it "breaking down" so often, most of the time it's not really breaking down. It's simply cascading to a stop because either load or unload has gotten backed up (usually it's unload)
At full capacity, each side of Space Mountain is running 14 trains. That means that each rocket is released into the ride every 21-seconds. So, when a rocket comes into the unload platform, it has 21 seconds to unload before the next one comes in. When all is running smoothly, it's a ballet of rockets that are always moving, never really bunching up anywhere. There are enough brake "zones" at unload to allow two or three rockets to back up behind the one that's actually at the unload station. But after that, they run out of available parking slots. So, the next rocket, which would be somewhere back near the reentry tunnel is stopped at the brake zone before that. Then the rocket behind THAT one is stopped at the brake zone before that, and so on and so on until all rockets cascade to a stop. (hence the term "cascade shut-down") The system does what it's designed to do, and it's done in a safe manner.
So, the CM working unload is constantly aware of this time limit. If any rocket sits at unload for a full minute, the ride WILL shut itself down. Sometimes it's not just a single rocket, but a few rockets in a row, each needing a little more than 21 seconds to unload. Little by little, the rockets start backing up, the unload station can't keep up, and the inevitable happens.
After a shut-down like this, they need to clear the track out, rocket-by-rocket. They start with those sitting at the unload platform, advance those to the load area, and then walk the track backwards, releasing each rocket from its brake zone as they come to it. Eventually, all brake zones are clear and the ride re-opens.
Test Track actually operates in a very similar fashion. If something happens at the load/unload platform, there's only a certain number of slots the cars can park at before they back up out the thermal-image tunnel, and the cars on the high-speed loop need to stop themselves. But because the cars are powered and computerized, the CMs don't have to walk the track. The system and the cars can come back up on their own. The only time the CMs would have to walk to track would be in the event of a breakdown that requires an evac.
-Rob