The 'modulation' is nothing more than a repetitive signal which requires no external control. No need to use an AOM, a spinning wheel with a butterfly shutter is more than enough.
The DVD and BR's will happily modulate at that speed, so you don't need to do anything special there.
You will lose a lot of green power because it's outputting at such a low duty cycle, but that's seriously hard to avoid. I've been experimenting with overdriving a green when it's running on lower duty cycles, but it's quite a trade-off between risking COD and losing output power.