There are a number of biographies of Wernher von Braun (became a naturalized citizen in 1955), my favorite being Von Braun: Dreamer of Space, Engineer of War by National Air and Space Museum curator Michael J. Neufeld.

The other most-covered Paperclip scientist is Arthur Rudolph (naturalized 1954, citizenship renounced 1983). The only biography I found of him is called An American in Exile: The Story of Arthur Rudolph by Thomas Franklin. Franklin was a newspaper columnist in Huntsville, Alabama--home of NASA's Marshall Flight Center and the Redstone Arsenal. As you might guess from the title, it is heavily biased towards Rudolph, as Franklin wrote the book following substantial one-on-one interviews with Rudolph in exile in Hamburg in the late 1980s when he was trying to clear his name.

There are a couple of books that cover some of the Paperclip scientists without being full-fledged biographies, as well as other former Nazis who were protected by the US military and intelligence communities. These include Operation Paperclip by Annie Jacobsen, The Nazis Next Door by Eric Lichtblau, The Rocket and the Reich by Michael J. Neufeld (mostly focused on ~1928-1945), Dark Side of the Moon by Wayne Biddle, The Paperclip Conspiracy by Tom Bower, and Blowback by Christopher Simpson.

As far as their acceptance into the scientific community was concerned, it went fairly smoothly--for a while. Even while World War II was in progress, many strategic thinkers saw the Cold War coming, and there was a scramble in the years after the war by the Western Allies to get as many German scientists and engineers as possible to keep them away from the Soviets. The price of that, however, was that all of their possible crimes were swept under the rug. In fact, Arthur Rudolph was subpoenad to appear as a witness in the Dora Trial (covering the concentration camp where the V-2 was produced after they moved production away from Peenemuenda, which was vulnerable to aerial bombardment). The US Army was afraid that he would say something self-incriminating, so they worked out a deal for him to be interviewed at Fort Bliss where he was living and his testimony to be submitted as a transcript.

Over the course of the 1950s and 1960s, no one really thought twice about what the German scientists/engineers had done during the war (except for satirist Tom Lehrer, who wrote his famous Wernher von Braun Song, and in a way Ian Fleming, whose 1955 James Bond novel Moonraker centered around former Nazi rocket scientists secretly working for the Soviets). But starting in the late 1960s and continuing in the 1970s, several former prisoners of Mittalbau-Dora Concentration Camp, mainly Frenchmen who were members of the resistance, wrote and published memoirs about their wartime experiences, and names like Wernher von Braun and Arthur Rudolph popped up in them. These included Planet Dora by Yves Beon, and Dora by Jean Michel. The memoirs came to the attention of the US Department of Justice and they began an investigation in 1979. Von Braun escaped scrutiny because he had died in 1977. They brought Rudolph in for three interviews, and in 1983 he agreed to renounce his US citizenship and leave the country in exchange for retaining the citizenship of his wife and children and the continuation of his Social Security benefits. He spent the rest of his life trying to clear his name, to no avail, and died in 1996 still proclaiming his innocence.

In the late 1980s, Michael J. Neufeld found a 1944 letter in a German archive that Rudolph wrote to the upper-level management at Peenemuende. He had toured a Heinkel aircraft factory that used concentration camp prisoners as laborers, and he enthusiastically endorsed this program and recommended that such prisoners be used to build the V-2.