It is possible to get minor leaders or even "random alignment" leaders by going to the custom game window and selecting the "Unrestricted leaders" game option and choosing a civilization but not a leader. From looking at the code I think that this problem was present before the changes in r1280.
I'm attaching a rework of the random civilization/leader assignment code in CvGame::init. Besides fixing this issue, it also allows to select a specific civilization and an alignment by choosing the civilization you want and one of the "random alignment" leaders.
This code seems to be broken when Unrestricted Leaders is off. When you choose a "random leader by alignment" you get a random leader regardless of the alignment. I'll try to see why this happens and I'll upload a new version once it is fixed.