Well I can't explain why moving armies through your vassals' land would make them hate you. It happened to me when I crusaded through the Moors' lands, and went down all the way to 'Abysmal'. The funny thing was that on the return trip, it didn't happen again. So I put it down to crusading in a Muslim faction's lands.
I also make it a point to ignore my vassals for the most part after I have established a client kingdom, except when giving regions. This will deny them opportunities to cancel the vassalage.
Even if relations are bad, it will go up over time, even on VH, because you have alliance, trade rights, and military access with them. You can also give a token tribute to them for 300 turns.
As far as I can tell, the AI can't resist free lands, possibly because of my high reputation.
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