After initial silence, we seem to be getting a fair amount of response on this—see John Sides (with continuing coverage) and Henry Farrell over at Monkey Cage—including, impressively, support at The Economist.
Some of this analysis seems spot-on; other responses—I trust you folks who were enthusiastically endorsing hurling obscenities at Coburn are aware that these all end up in his briefing papers the next morning, but assume, presumably, that he will be is absolutely petrified at the rhetorical intensity of your opposition—make me want to just say, well, if this is the best the community can manage, the program deserves to get cut.
Hey, send the geezer out to pasture, eh?—guys just wanna have fun, and to hell with the consequences.
A couple reactions nonetheless:
1. Those who think that NSF is going to play little Jedi mind tricks with the national security and economics exception are living in a fantasy world. While I’ve not talked with anyone at NSF since this hit, my guess is that they are in serious damage control mode and their single greatest fear is that this is going to spread to other programs, either within the social sciences or to other topics, climate change undoubtedly being the prime target.
I’ve had a lot of experience with NSF over the years, and have a great deal of respect for the institution. Many of the comments are treating it as though it was Officer Krupke in West Side Story, or Inspector Jacques Clouseau of Pink Panther fame. It’s not: it is a large, mature, and sophisticated bureaucracy—“bureaucracy”: aren’t political scientists also supposed to know something about those?—with a complex relationship with Congress, and a collective sense of responsibility for basic research in the sciences generally. They aren’t going to regard this as a funny little game.
Which, in turn, means that yes, this is going to have consequences.
2. Splitting off the national security and economic research communities is significant. I’m not suggesting that I could personally turn this thing around—though I conceivably could do something more effective than on-line petitions or profanity-laced diatribes—but I would happily lobby for the policy importance of the NSF-funded work I’ve been doing. The [hypothetical] response now?: “Yes Phil, we agree entirely, and that’s why we put in the national security exception. Thank you for your service. Oh, and loved your critique of garbage can models in Seven Deadly Sins…” Same with anyone doing domestic, comparative or international political economy; same with anyone doing comparative political violence, and possibly comparative democratization.  What you’ve got left is, in fact, pretty much U.S. electoral, institutional, and [yes] Congressional studies, and whatever aspects of comparative politics can’t be plausibly—emphasis on plausibly—argued to have security or economic consequences. 
If Coburn’s target is legislative studies—we still don’t know—and I were looking at this from the outside (which, now, I pretty much am), I’d say that was a really slick move.
3. I quit the APSA about three years ago, after receiving an extended lecture from Michael Brintnall on the links between open access journals and the end of civilization, and the Perestroikan/White Citizen’s Council successful blackballing of Walter Mebane, so again, I’m on the outside here as well. Still, for years (and thousands of dollars paid in inflated dues), I listened to the APSA extoll its superb access to Congress through the legislative fellows program, and this in turn justified their need to be in Washington rather than, say, Tucson.  IMHO, if APSA were doing its job, this issue would not have made it anywhere close to a floor vote—similar efforts have been pushed back several times over the past thirty years—and the response would have not been a petulant press release that may well be making things worse. Jennifer Victor outlines a lobbying strategy—based on, hey, research by political scientists [!]—that in all likelihood would be highly effective, but requires coordination and initiative. I can only hope that something is going on in the background, but I’ve seen little evidence of this. 
1. Not trashing Tucson: that is where the much more reasonably priced Middle East Studies Association and International Studies Association, professional memberships I’ve maintained, are located.
2. Same for MPSA, though it was long ago relegated to shilling for the Palmer House and maximizing the number of second-year grad students it could stuff onto panels, at least in IR. Though at least is in Bloomington, Indiana, not Dupont Circle.
3. IR and much of comparative being further distracted from the debate by the fact that we are all desperately trying to finish our ISA papers. Unless procrastinating by writing blog entries.
4. Methods, measurement and statistics?: there’s a separate program for that. Those who see this move as the end of the Society for Political Methodology: isn’t going to work out that way, and besides, about half of the SPM oligarchy now seem to have joint appointments in professional schools anyway. Same for “law and society.”