Welshman Bale withdrew from the Games with a back injury, but played in a friendly for his club before Britain's first match against Senegal on Thursday.
Blatter suggested earlier this week that football's governing body could ban the 23-year-old winger if the British team lodged a complaint.
"I understand the response from some football fans who were hoping to see him play as part of Team GB," Moynihan said at a news conference in the Olympic Park on Thursday.
"My view is different. I welcome the fact that he has returned from injury earlier than expected. I don't agree with Sepp Blatter's comments about banning him.
"I think Sepp Blatter needs to get closer to Team GB."
"I think there's a very simple difference. Phillips was selected for the team, Gareth wasn't," Chef de Mission Andy Hunt said.
"All I would say is that [coach] Stuart [Pearce] is very comfortable with the team he has and we're looking forward to them starting their first match.
"Stuart made his selections based on fitness and form, you can't predict a recovery period from an injury.
"Gareth's missing an amazing opportunity which I'm sure he will look back on and be tremendously disappointed about."
