It sounds like the issue is this:
1. UA Changed their pricing around for Government fares.
2. UA Loyal flyers in SAN (in this case) are now "stuck" flying another airline because of this
If you were a kayaker who didn't care about which airline you flew with, then this wouldn't be an issue. It sounds like the issue comes into play when you are forced to make a decision about your FF loyalty that you'd rather not make.
Does that sound right?