Navratilova said the Australian great, now a church pastor, was "all about Adam and Eve, not Adam and Steve" in her views, which attracted controversy and protest threats on the eve of the year's first grand slam.
"You know, it's a personal issue," said Navratilova, a long-time critic of Court's along with Billie Jean King, who is also gay.
"Clearly, Margaret Court's views that she has expressed on same sex marriage, same gender marriage, I think are outdated.
"But it's not about any one person. It's not about religious rights, it's about human rights. It's a secular view, not a religious view.
"She's only seeing it from one viewpoint."
But the 18-time grand slam winner described it as an "honor" to play on Margaret Court Arena in the Open's women's legends doubles competition.
"I have spoken to her years ago, but, you know, she was all about Adam and Eve, not Adam and Steve," Navratilova said.
"She repeated that about four or five times, so I just felt I couldn't get through to her. Maybe she thought she could get through to me."
Activists launched a Facebook campaign against Court, whose 24 major singles titles are a world record, and said they would protest at Melbourne Park against the former player, who defiantly vowed she would not be scared off.
There has been little sign of rallies at Melbourne Park although Britain's Laura Robson last week wore a rainbow hairband supporting equal rights. But she denied she was making a formal protest against Court.
Navratilova also said the women's game lacked big stars and said the current ranking system was weighted too much towards quantity of matches, rather than the quality of the opposition.
"Clearly nobody feels that (Caroline) Wozniacki is a true number one," she said, tipping Wimbledon champion Petra Kvitova for future glory.
"If we still had the same ranking system we were using six years ago when they were giving bonus points for beating players, Kvitova would have ended up number one because she had beaten more top players than Wozniacki."
"With the absence of Serena (Williams) playing enough, we need some superstars that you really feel like they're holding their own," she added.
"I think Petra has that possibility. (Victoria) Azarenka is coming up as well. She's playing good ball. Can't be overlooked. Although she's never been to a grand slam final, but she's looking the part more and more."