You don't.

Well, you can capture their last remaining province (AFTER taking Kyoto) and vassalize them. That way you avoid the diplomacy penalty that is realm divide and can keep them as vassals. If you carefully make love not war before realm divide (i.e. marriage treaties, alliances, trade agreements) you might be able to keep 2-3 loyal allies, even after realm divide, provided you're willing to constantly throw money at them. The rest will just hate you and there's not much you can do about it. Take it as a challenge.