Eventually the NIF got around to publishing a rebuttal to the Im Tirzu report. You can download the full report here, but it's in Hebrew only - which is odd, since these organizations publish almost all their documents in English.
It's important that the NIF responded, because their initial reaction was to use legal measures to shut down the Im Tirzu campaign, hardly an honorable response that, and then to concentrate their ire on the form of the criticism against them, not its substance. Yet their responses now are hardly satisfying.
I haven't read the entire 112-page ImTirzu report. My understanding of their thesis, however, was never "absent NIF there'd have been no Goldstone Report", which would have been a silly idea. What they were claiming was that the NIF-NGOs, unlike the other Israeli entities cited by the Goldstone Report, set themselves firmly in the critical-of-Israel camp. This claim is so obviously true it's hard to see why anyone would even try to refute it; may I remind us all that back in June 2009, as the Goldstone team was just beginning to operate, a coalition of these Israeli NGOs essentially said this themselves in a document they submitted to Goldstone and put on their websites (here's the ACRI version, and here's my reading of that document, from August).
The English version of the NIF response is here, and a synopsis of the 29-page rebuttal report is here. It just so happens that I responded to the synopsis on February 10th, the very day it was posted, and my response is still there, so I don't need to repeat it here. As for the NIF response, it seems to me mostly irrelevant. No-one is claiming the NIF does nothing of any value in Israel, rather that they do good and bad simultaneously; enumerating the good is therefore besides the point. Except here:
We challenge Im Tirtzu, NGO Monitor and other NIF critics to demonstrate the value of their contributions to Sderot.Why are the actions of their critics relevant? It's the NIF that needs to respond, not their critics.
Since the NIF response enumerates fine things they've done in and around Sderot, however, they do open themselves to an additional line of questioning: Have any of their NGOs ever, at any point since 2001 when the attacks on Sderot began, demanded of the Israeli government that it protect the Sderotians from the infractions of their human rights? The NGOs under attack produce an endless stream of reports, court petitions, demonstrations and so on demanding that Israel treat the Palestinians better; have they ever taken similar action so that the Israeli government protect Israeli citizens?