+1 to Hypothesis and similar tools kind of already doing what you're thinking of. I would use the energy to contribute to it:
https://github.com/hypothesis/client, and it's possible that you might find ways to optimize it for wikis via a gadget.
They've probably solved the "parent paragraph updating" problem you mentioned here. So at the very least you can find inspiration there. But I imagine the issue of storage and all that is tricky. There was a W3C working group that the Hypothesis people were part of, I remember we half-heartedly wanted to join but never did.