Run a MongoDB configuration server without 3GB of journal files

Yes - there is a way to minimize the default size of the journal files, subject to a couple of caveats. From the MongoDB configuration documentation:

To reduce the impact of the journaling on disk usage, you can leave journal enabled, and set smallfiles to true to reduce the size of the data and journal files.

Here is the smallfiles config information:

Set to true to modify MongoDB to use a smaller default data file size. Specifically, smallfiles reduces the initial size for data files and limits them to 512 megabytes. The smallfiles setting also reduces the size of each journal files from 1 gigabyte to 128 megabytes.

Use the smallfiles setting if you have a large number of databases that each hold a small quantity of data. The smallfiles setting can lead mongod to create many files, which may affect performance for larger databases.