There is so much "stuff" in this article, it is difficult to know where to begin! I think a non-partisan review of intelligence activities is in order. A crime is a crime, regardless of political party.
First, you need to review the laws that are currently on the books against torture and other illegal behavior, and do some training to make sure the various agencies and departments understand the rules of behavior, along with the legal consequences of bad behavior. You enforce the laws on the books! These were the laws, when those crimes were committed.
Second, you make presidential findings an impeachable offense. Everybody obeys the law, or they go to jail.
Third, you need a variety of opinion when dealing with intelligence assessments. Each agency needs to do their own thing, and heads of agencies should meet regularly to share information with the national security adviser. Everybody's opinion is valuable, and massaging this information into one partisan stew is not allowed.
Fourth, lower-ranking members of the agencies should communicate laterally in sharing information. Whoever initially acquired the information should lead in exploiting any actionable intelligence taking into considerations their resources. I worked in communications in the US Army in Europe, and we often communicated with the British Army. This is no big deal.
Fifth, covert action became fashionable during WWII, and the CIA's ancestor the OSS did a lot of it. In the modern world, as with optional wars, covert actions have unforeseen consequences.