Paul Pillar is a highly respected but now intelligence analyst. He was the National Intelligence Officer for the Near East and South Asia from 2000 to 2005.
"The main impact of this affair on intelligence work is not likely to involve the Arab-Israeli dispute, even though it is what concerns those who shot down Freeman. The most important facts and patterns about that tragic conflict are an open book; we don't need the National Intelligence Council to tell us the implications of continued expansion of Israeli settlements, the consequences of rockets fired at Israelis, or the effects of unending occupation on the emotions of those under occupation. The main effects will instead come, perhaps subtly and invisibly, with other issues on which a dominant policy imperative emerges -- such as the Iraq war, though not necessarily with as intense an environment as what the Bush administration created to sell that initiative. The effects will consist of intelligence officers being at least marginally less willing than they otherwise would be to challenge the ethos surrounding the policy and to point out ways in which the policy might be misguided. Some such policies will be misguided, will come a cropper, and will lead to the usual recriminations about how intelligence failed."
"When that happens, those in Congress and elsewhere who acquiesced in the character assassination of Chas Freeman -- or even worse, participated in it -- should ponder two things about intelligence. First, they should ask how they could expect intelligence officers to show superlative courage in bucking political orthodoxy when they showed so little themselves. Second, they should reflect on how their own pusillanimity in the face of the lobby that gunned down Freeman has made it even less likely that intelligence officers will be able to muster such courage in the future."
Also: Freeman on NPR.