The actor, who played Sansa Stark in the hit HBO series, branded the petition “disrespectful”, after it gathered over a million signatures prior to the last instalment airing.
The Change.org post calls for the final series to be remade “with competent writers”, with 1.3m fans having now signed as of Tuesday morning.
Speaking to The New York Times, Sophie said that she is “not surprised” there has been a backlash.
“People always have an idea in their heads of how they want a show to finish, and so when it doesn’t go to their liking, they start to speak up about it and rebel,” she said.
“The thing about Game Of Thrones that’s always been amazing is the fact that there’s always been crazy twists and turns, right from season one with Ned’s beheading. So, Daenerys becoming something of the Mad Queen — it shouldn’t be such a negative thing for fans.
“It’s a shock for sure, but I think it’s just because it hasn’t gone their way.”
She continued: “All of these petitions and things like that — I think it’s disrespectful to the crew, and the writers, and the filmmakers who have worked tirelessly over 10 years, and for 11 months shooting the last season.
“Like 50-something night shoots. So many people worked so, so hard on it, and for people to just rubbish it because it’s not what they want to see is just disrespectful.”
Sophie’s comments echo those made by other cast members last week.
Bran Stark actor Isaac Hempstead Wright branded the petition “ridiculous” and “absurd”, while Jacob Anderson – aka Grey Worm – called it “insulting”.
It was set up after the penultimate episode, which saw Daenerys’ decision to torch the city of King’s Landing, along with the innocent people in it, with many fans claiming it was a betrayal of her character.
Arya and Gendry’s romance has also been a topic of debate, as has the decision to kill Cersei and Jaime Lannister with a load of falling rubble.
The TV version of Game Of Thrones overtook George RR Martin’s books quite some time ago, despite the writer being five books ahead of the show when the first season aired.
George has made no secret of his disappointment at the timeline, which left him no choice but to tell the showrunners plot secrets in order for them to finish the programme without any source material.
Meanwhile, Emilia Clarke, who played Daenerys, has spoken of the changes she would have made to the final season.