A schoolgirl's friendly visits with her Panamanian pen pal, Gen. Manuel Antonio Noriega, have her neighbors and her Congressman shaking their heads. ''If it was my daughter, she wouldn't be going,'' said Virginia Paulson, a Councilwoman here, after the 11-year-old girl, Sarah York, left last week for her second trip to Panama. Sarah's parents declined to discuss the issue.

Last Wednesday, Sarah and her father, Mitchell, a prison guard, turned up beside General Noriega, who had just survived a coup attempt. The military ruler called her a ''meritorious daughter'' of Panama City and as an example of ''the truth of the United States, purity not hatred.''

After meeting with the general, who is wanted in the United States on drug-trafficking charges, Sarah repeated her support for him, saying that he was ''very nice'' and that she did not believe ''the bad things papers in the United States say about him.''

Representative Bob Davis, Republican of Michigan, said Sarah's visits to the general put the United States in an awkward position. ''To have one of our little citizens go down there and be treated well is kind of an embarrassment for our Government,'' he said. ''It sends the wrong message that we, or some people in this country, say Noriega is an all-right guy.''