Peter Sowrey tried to change the venue, or at least have a "B plan" but says "I was told to gag myself on the subject."
Andy Hunt took over just two weeks ago as the new CEO, and sailing is still scheduled to begin in August in the sewage-filled bay.
In interviews with The Associated Press, Sowrey and Hunt said the bay - overlooked by the famous Christ the Redeemer monument and Sugarloaf Mountain behind it - may give sailing the kind of television coverage it seldom enjoys.
It could also bring unwanted attention if sailors fall ill, or if floating rubbish - plastic bags to door frames to animal carcasses - fouls rudders and costs someone an Olympic gold medal.
Sowrey proposed moving the event to Buzios, a coastal resort about 160km from Rio that has been host to large sailing events. Of course, it's too late now for that change.
Sowrey, who left in December after only five months on the job, came to the governing body from the consulting company Accenture. He acknowledged he had little experience dealing with the politics that drive international sports federations. But he brought business acumen.
"The board felt I was way too aggressive," Sowrey said. "They basically voted me out. I didn't resign. The board finally told me to leave."
Sowrey said looking at Guanabara Bay on "fact-based, data-driven model we would never consider sailing in that quality of water."
Independent testing of Guanabara Bay conducted by the AP over the last year shows disease-causing viruses linked to human sewage at levels thousands of times above what would be considered alarming in the US or Europe. The tests include the venue for sailing, but also Rio's Olympic venues for rowing, canoeing, open-water swimming and triathlon.
About 1,600 athletes will compete in these venues during the Olympics, which open on August 5, and hundreds more during the subsequent Paralympics.
Experts say athletes will be competing in the viral equivalent of raw sewage with exposure to dangerous health risks almost certain. Many sailors have described the conditions as "sailing in a toilet" or an "open sewer."
Viruses like those in Guanabara Bay can cause stomach and respiratory ailments that could knock an athlete out of the Olympics.
When he first learned of the AP analysis, Sowrey supported the same kind of independent viral testing. But he was nudged to support the position adopted by the International Olympic Committee, the World Health Organization and local organisers; that the bacteria-only testing was sufficient.
"I was just stepping on toes," Sowrey said.
Hunt has been weaned on sports politics. He was the CEO of the British Olympic Association, and the BOA delegation head for the 2010 Vancouver Winter Games, and the 2012 London Olympics.
"It (Guanabara) is not ideal," Hunt said. "For one moment I'm not saying it's ideal, but I do think there's a huge amount of effort and attention going into this to ensure the safety of the athletes.
"I'm completely aware of the possibility and the challenge of how this (Olympic sailing) might get portrayed," Hunt said. "The ultimate test - if we have delivered a great regatta - will be the response from the sailors."
