So, before I go too much farther, I just submitted the patch above. Took a couple of tries before I got to this solution.
Basically, I just made a wrapper around the Configuration class that comes from the (older) hadoop code. The wrapper has one extra method on it, that missing getInstances(). See the JavaDoc in ConfigurationHolder for details, but basically it tries to maintain backwards compatibility with the older APIs (in the com.cloudera packages), and be compatible with anything external, while still allowing use of that missing method.
The tests all pass, but I don't have a very good environment to actually run this code (hence my work to make sqoop compatible with my cluster!), so it could use some exercise.
Anyone want to take a look at this? Shoot arrows at it, maybe?