If you know what to do with a write to the zero page, I presume you know how to write NES code. If you need help modifying the NSF driver, feel free to ask.
This would be easy to add, but would be even faster to customize the existing E command (as you pointed out, for example), one option would be to use it on the triangle channel where it has no effect (as long as it's not zero). Then change the behaviour in the player code.
I'd like to second the notion of this. I'm not as well versed in the know how, but all I know is that in music with higher BPM and maybe some tempo changes, having the ability to re-synchronize the timing would be very much appreciated.
If this is not the same issue, then I apologize, and I can start a new topic for it.