Peace prizes are different from science prizes. The Soviet Union had no problems with its scientists getting science prizes. It did sometimes had problems with letting them leave the country to actually receive them, of course.
While your disambiguation is valid, they very much wanted to minimize the potential fallout from individuals staying in, say, a Norwegian hotel and sampling the local culture only to return and speak fondly of said trip "beyond the curtain". Usually this was outweighed by the national prestige (and subsequent propaganda opportunity) from having a Soviet Nobel recepient but the KGB had an extremely heavy hand in deciding who got to go, regardless of scientific breakthrough.
