Let's just look at Allende since you've emphasized him. Whatever his bonafides may be, and I find many reasons to support him (not least of which is that he was elected by Chilean voters in well-conducted, transparent election), he was openly proud, as were the majority of Chilean voters who elected him, of the support he received from Cuba and the Soviet Union. It was part of Allende's new foreign policy that included a state visit from Fidel Castro himself.

There was no need for paranoia by the CIA, because Allende's foreign policy and domestic policy already publicly announced socialism and supporting policies of land confiscations and redistribution of anything over 80 hectares and similar initiatives, and he came to power in a a election on making a hard shift toward socialism and affinity toward Cuba and the USSR, not hiding it all.

The reason the CIA got involved in overthrowing Allende had nothing to do with falsely making Allende out to be an extreme socialist leader of a potentially new wave of anti-US governments in Latin America. Allende was openly exactly that kind of leader and had openly campaigned on that platform, similar to the leaders of Ecuador, Venezuela, and Bolivia today. That's why such evidence does not support an argument that US intelligence agencies do not know how to do effective counterintelligence work.

Similarly with Trump today, he actively campaigned and won an election where he argued for supporting Russia in Ukraine and Syria instead of opposing, and his affinity with Russia has been public knowledge. The only additional information intelligence agencies have brought to bear is that Russia has expended effort to influence the election, on his behalf.

Whether Trump knew this and coordinated with Russia on this or not is immaterial, as is whether Russia could extort him to control like a low-level agent or not. What we do know from all that has been publicly acknowledged so far is that the Russians helped put Trump in the White House, so that must serve their interests.

This means, getting back to the argument of Luis's post, that we cannot use historical interpretations of national interests to explain what the US is doing anymore. We must include Russian interests in that analysis, and while supporting the EU and its development has always been an explicit part of US foreign, economic, and security policy since WWII, the fact that it has always been contrary to Russian interests have much more to do with the US putting anti-EU diplomat as its envoy, not historical US interests.