How to isolate 1 MongoDB config server
Yes, you can simply stop one config server, upgrade and restart it. That is one of the reasons why there are three: even when taking down one, there are two others to read from, so one might fail.

A few things to keep in mind, though:


When one config server is down, the cluster meta data is read only: no chunk splits or migrations during that time. So in order to prevent JumboChunks, you better hurry a bit.
Talking of JumboChunks: you should check your cluster for them after update
As for the order: Start with the last server in your configdb string, finish with the first
Always, Always, ALWAYS read the migration guide of the version you are updating to