I'm having a hard time visualizing your problem. The
pads that came with my Tektro cantis are only 10mm high. Surely, your rim has more braking surface than that, so I'll assume I don't understand.
I looked at the
Kool Stop BMX pads on their web site, and I can't see a particular difference between those and standard V-brake pads, but they look like they'd work with your brakes.