"This was never our reporter's intention, of course," Avlon wrote.
"No names were ever used and some of the profiles described were of straight women.
But there was a concern that even mentioning the home nation of some gay athletes could compromise their safety. We apologise for potentially jeopardising that safety in any way.
"As a result, we have removed all descriptions of the men and women's profiles that we previously described."
America's Society of Professional Journalists was quick to criticise the story as well.
"The athletes adversely affected by the story also deserve an apology," wrote Andrew Seaman, who chairs SPJ's ethics committee.
"Such a story has no place in a modern media organisation."
The story has now been removed from the site and replaced with a note from the editors.
"It's up to us to deliver stories that are so clear, they can't be misinterpreted - and we clearly fell short of that standard in this article," Avlon wrote.
"Accordingly, we have made some editorial changes to the article, responding to readers' concerns, and are again sorry for any upset the original version of this piece inspired."