You need to rescue a scientist who uncovered reaper tech that told her that Reapers would arrive in 2 days in a system with a mass relay that would allow them to go anywhere they want. After that, it turns out she's indoctrinated, but that she and her team had a plan to destroy that relay with a masssive meteor. They stopped because the energy released by the relay would destroy a batarian colony near it. So Shepard reactivates the facility, crashes the meteor into the relay, kills 300k batarians, delays Reaper attacks for at least a few months.
I think you misunderstood something. Or the way you typed it reads funny to me.
They did not stop because of the Batarian deaths. They stopped because of the indoctrination. The deaths of the Batarians is practically an incidental matter. And a plot hook for ME3.