Sure. Also, I think that all the data will not only be for connectomics aka mapping brain connections per say; you can extrapolate a TON of other science from stacks of EM micrographs, so if all this data is shared with other researchers, we can:
1. map brain connections
2. see what other changes occur compared to control. For ex: changes in volumetric parameters; organelle size, synapse density. Tweak some methods and youll also see protein localization and identify cells.
3. Reconstruct all that to make awesome 3D models
This is a lot work and currently the problem is in computation.
As for the biological noise problem, I agree we haven't a clue about how all the different cells of the brain work in concert; I also think a sure-fire way to create even more biological noise is to approach the problem from a biochemical or molecular perspective: with all the different cells in the brain it will be even more difficult to put all that data together as a whole once we have all the molecular pieces and most likely, they will not coincide with each other.
Electron microscopy, on the other hand, provides data that you can see and use readily.