Their worry over traffic safety stems from their claim, backed up by official statistics, that the intersection is one of the borough's most dangerous.
The residents also asked Rutter's officials to limit the hours of the station, eliminate glaring lights and loudspeakers on the gas pumps.
Kim Tartaglia, of 8 W.Third St., said Rutter's won't have to ask its neighbors to be "quiet at night, tell us our lights are glaring in your window, keep the noise down or complain to your neighbors that any of us has moved into your neighborhood and built a steel and glass skyscraper."
Gary Patel, who in April opened Waynesboro Food Mart, a gas station and convenience store at 806 S. Potomac St., told the council that if Rutter's is allowed to open it will put him out of business.
The planning commission recommended approval of the project on July 27. Commission member Deborah Hoff, whose law office is across the street from the site, voted no.
The council held off voting for 15 minutes Monday to go into executive session, they said, to get an opinion from Borough Solicitor D. Lloyd Reichard II.
Reichard advised the members when they reconvened that they had to approve the project because it met borough zoning and subdivision regulations.
Rutter's attorney, Gavin W. Markey of York, Pa., urged approval, saying the company complied with all zoning and subdivision ordinance rules that applied.
Councilman Richard George made the motion to approve the project. He was seconded by Ward II Councilman John Cook. The Rutter's property is in Ward II.
"I was voted into office to maintain compliance with the ordinances," Cook said after the meeting.
According to Rutter's plans, the main entrance will be off South Potomac Street with limited access in and out on West Third. A third entrance will be on Philadelphia Avenue on Rutter's north side.
The corner property covers about 6,300 square feet. Plans call for a convenience store, 12 gas pumps and a canopy.
Tim Rutter, company treasurer, sat quietly while residents criticized the project. He said after the vote, "there are two things that people hold dear, their families and their homes."
Any commercial development will bring change to a neighborhood, he said.
"This is a free society. People can express these opinions," he said. "I just don't happen to agree with them."