President Reagan, responding to a last-minute appeal from Atty. Gen. Dick Thornburgh, vetoed legislation that would have given major new protections to federal workers who expose fraud and mismanagement. The surprise move to pocket-veto the legislation, which passed the House 418 to 0 and the Senate by unanimous voice vote this month, came after four years of intense negotiations in which congressional leaders thought they had achieved a compromise acceptable to the Administration. Congressional negotiators expressed outrage at what they viewed as the Administration’s betrayal. Reagan, in a two-page statement issued just hours before a midnight deadline for signing the legislation, said the measure had constitutional problems and would hamper legitimate discipline of federal employees. He said he would submit his own bill in January when Congress convenes.