From the comments, the intrepid Cap'n Transit has some creative suggestions for the MTA to mitigate the impacts of the Smith/9th station rehab (station closed for nine months . . . and that's if there are no delays).
First things first: MTA has to do a better job of outreach on a project like this. The Carroll Gardens Neighborhood Association didn't have any warning that this was coming: the first any of us heard of it was from the Metro article last week. But it's not too late. The station work is expected to take place in 2010; there is still time to get community input on the necessary mitigation efforts.
First off, running a shuttle bus directly from Smith and Ninth into the Battery Tunnel and out to the Fulton Street Transit corridor is a must. Second, there should be some shuttle service to 4th Avenue for those who are doing a reverse commute. Simply running a shuttle back and forth between Carroll Street and Smith/Ninth is unacceptable.
Long term, as Cap'n Transit suggests, a tunnel would be nice; however the limiting factor (besides the obvious cost) is topography. The train would have to take a pretty massive dip under the Gowanus Canal, and the relative elevations at Carroll Street and in Windsor Terrace are pretty high. Thus, the ride would be a bit of a roller coaster along that stretch, and steep tunnels are tough for the trains to handle.
I could be wrong about that last bit, I understand that to be the problem.