The Realm Divide diplo-penalty is initiated both when you reach the clan fame threashold AND when you capture Kyoto, regardless of if one of those things has happened already. So do both before setting up 'safe' vassals for post-RD trade, or make sure you've got some allies with ~150 relations before you divide. To clarify, if you set up vasslas after realm divide and then capture Kyoto, they'll start getting the penalty at that point. I've never captured Kyoto before the clan fame has kicked in so I don't know if it works the other way around, but I have set up vassals before capturing Kyoto, and the realm divide diplomacy counter started for them on that turn.