This is a common tactic in English writing - a paragraph has certain 'parts'. The first sentence generally talks about what the paragraph is 'about', and the middle sentences give supporting evidence (or explanation) to the first sentence. The last sentence, when used like this, will often refer back to the main idea of the paragraph.
In this example, the 'this' refers to the firing of Harrison Shepherd.
This piece is written with bias - meaning that it presupposes the conclusion without giving any evidence to reach that conclusion. The novel is about a period of time in American history when being 'un-American' was very nearly a crime, and many people were persecuted for 'un-Americanism' while having done nothing wrong.
There are some clues to this in the paragraph. It mentions 'misdeeds', yet offers no concrete accusation or charge, and also mentions that his role is unclear. As you noted - if there is no proof of espionage, how are they driving out potential spies? You are not actually confused at all, you are correctly interpreting the passage, but the passage is written from the point of view of Myers (it sounds like), where the assumption of guilt is present without evidence.