Raspberry Pi stereo camera frame synchronization/genlock (video or still image)
I think your both options/ideas (Pi and Compute) can work. 

Raspberry Pi GPIO is fast enough (10MHz+), reading GPIO input state every millisecond will be no problem at all.

If you want to process data on Raspberry Pi with OpenCV or something like that - don't expect too much, Pi CPU is not that fast as some people think. Do some experiments with pre-recorded video or images and see how much computing power you have.

If you find that Raspberry is not fast enough - you can use something like this (for image processing):

Nvidia Jetson TK1 Development Kit

- NVIDIA Kepler GPU with 192 CUDA cores
- NVIDIA 4-Plus-1 quad-core ARM Cortex-A15 CPU
- 2 GB memory, 16 GB eMMC
- Gigabit Ethernet, USB 3.0, SD/MMC, miniPCIe
- HDMI 1.4, SATA, Line out/Mic in, RS232 serial port
- Expansion ports for additional display, GPIOs, and high-bandwidth camera interface


I don't know much about this, just read somewhere about these Nvidia products, but it cost less than Pi Compute module (192USD is 115GBP?), and there is a lot more computing power.