The Retake Mass Effect fan campaign claims to have raised $28,000 (£18,000) for the Child's Play charity in a bid to convince developer BioWare to take its cause seriously.
"We would like to dispel the perception that we are angry or entitled," reads the group's mission statement. "We simply wish to express our hope that there could be a different direction for a series we have all grown to love."
However, Hudson is standing by the original finale, claiming that the "polarising" conclusion is what makes the story memorable.
"I didn't want the game to be forgettable," he told Digital Trends. "Even right down to the sort of polarising reaction that the ends have had with people - debating what the endings mean and what's going to happen next, and what situation are the characters left in.
"That to me is part of what's exciting about this story. There has always been a little bit of mystery there and a little bit of interpretation, and it's a story that people can talk about after the fact."
The BioWare executive went on to say that additional single-player and multiplayer DLC will be introduced to Mass Effect 3 in the future, and fan feedback will be taken on board during its development.
"We have some really great multiplayer content and some really great single-player content coming over the air and their feedback will become part of how we design that," he added.
Mass Effect 3 is available now for Xbox 360, PC and PlayStation 3.
> Read our review of 'Mass Effect 3'
> 'Mass Effect 3' leads all-formats chart: biggest release of 2012
Watch the launch trailer for Mass Effect 3 below: