As always, in a sustained movement for political change, the question is not merely the conflict of the moment but establishing reputation for the future. To take an example from the media reform movement -- I was giving a talk at the FCC on the impact of the blogosphere and one person challenged my statement on the influence of the media reform movement by observing that we only managed to get the national ownership cap reversed in 2004. Yes, I replied, but when the court reversed the FCC and the matter came up again on remand in 2006-07, the framing and structure were entirely different. The sweeping reform of '03 was not even attempted, and only a relatively minor change to one rule occurred. Because in '06, people remembered what happened in '03 and shaped their perception of what was politically possible accordingly.
Obama and the Dems generally are discovering that the netroots have become as essential to victory as any of the other major constituencies. Perhaps more so, as they provide significant money, volunteer labor, and cutting edge/new media PR. At this point, Obama would find it very hard to reverse himself again. Having staked out the position that the current bill is an appropriate compromise, he cannot back away easily without appearing utterly craven and without judgment, since he should have gotten it right the first time. But the Democratic leadership have options -- up to and including stripping the immunity provision or refusing to bring the bill to a vote. They can also try to persuade/browbeat the netroots into submission. But it doesn't work that way, as they have discovered.
So realistically, either Obama can persuade the Congressional Dems to back off (at least until after the election), or he can take his licks in this round and do better going forward. Meanwhile, McCain is facing a similar insurgency from the Ron Paul faction, which is threatening to break off and support Bob Barr. That gives the R leadership its own incentive to pull back (at least until after November).
My instinct of the moment is that when Congress returns, it will focus on other issues and leave FISA until after the election, at which point it will find its way into an appropriations rider. Obama will duly vote against cloture and against the bill, but the numbers on the R and D side in a major approps bill will make this a mere symbolic token of resistance. But while the net roots will likely ultimately lose on the substance, they will win on the larger issue of Feld's Law of Political Power: Your political power is directly proportional to your perceived ability to cause pain. It is a lesson a new Congress will remember as it heads into the '08-10 session.