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."
The BOA said the situation with Bale was different to that of triple jumper Phillips Idowu.
Idowu pulled out of training camp through injury and the BOA have demanded to see his medical records to ensure he is fit to compete.
"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."
