I think the lying occurs higher up in the command structure where some intelligence is omitted from consideration because it doesn't fit the narrative the higher-ups are pursuing. I suppose there's a question here about who, exactly, is involved in this process of filtering out inconvenient information. Are those people part of the intelligence agency or not? This is a tricky question but, even if they are part of the intelligence agency, the pressure to omit comes from the executive branch. The NSA/CIA/etc aren't pursuing a pro-War policy...the executive branch is.
For example, imagine someone in the CIA is asked to provide a report about the likelihood of Iraq having radioactive material that could be weaponized. This person performs diligent research and produces, to the best of their abilities, a factual report. The executive branch presents this report as a "slam dunk" which shows that Iraq has radioactive material. Who lied?
Toward the end of your post, you blur the distinction between "lying" and "having a duty to contradict false claims". I'm only talking about lying although I agree that people do have an imperfect duty to contradict false claims.