It appears that this relationship is headed downhill and they are perfectly ok with that. To my untrained eye, US appears to be readying to downgrade the relationship with India ahead of the expected government change in 2014. This downgraded relationship would be a new datum from which the new GoI will have to negotiate and make concessions to US in order to restore the relationship to levels before this outrage.
We might say they are preparing the ground for a Modi PMship, during which India will be turned into a "bad actor" in US and much of world media, worthy of US punishment. That would be a way out of having to walk back the insult to Modi.
Would the US go to that extent just to avoid saying to Modi, "what has happened has happened, let's make a new beginning?" (and I think Modi would be fine with that). I think it would. We mustn't underestimate the role echandee plays in the minds of the thekedars of the world, and wannabe thekedars like TSP.
Call this a modest ahead-of-curve prediction: Look ahead to a Modi PMship faced with color revolution by oppressed Muslims and "seculars", forcing him to either abdicate or take stern measures, the latter confirming the "bad actor" narrative.
Modi will need all the help he can get. I hope he and his team will exhibit the qualities of head and heart that the coming challenge will demand.