The most troubling aspect of this, to me, is the idea that these Sunni militias we're arming are summarily executing "suspected" Al Qaeda fighters. How does the US ensure that they are not just rounding up rival Shiite leaders? They don't.
One of the famous "benchmarks" is the disbanding of armed militias, and political reconciliation between Sunni and Shia factions. Is this serving to further that goal?