Ah-- I think the timing's a bit funny on that. They were going to punish her before she poisoned the Doctor, and the death date was 2011, not 1938. "He can't be dying now; it's a fixed point." I thought they just took the opportunity because she was right there. (Plus, the 6B trailer shows Madame Kovarian in a setting very much like the Luna University, so we aren't done with that yet.)

And here's my second, contradictory thought: Melody Pond killed the Doctor (poison), and that's why they punished her. But they didn't recognize her as River Song. Why not? Because Melody Pond's established timeline was up; she became River Song when she enrolled in the University.

I thought River was just talking about that immediate point-- in the future, they may well have decided that because the poison didn't work, a gun might.

So many unknowns, so many ways to interpret things. :)