The Leith boss has been holding training ground talks with his squad after they lost their Scottish Premiership place to Hamilton following a dramatic penalty shoot-out defeat in Sunday's play-off final second leg.
Ex-captain McPake and former Scotland international Thomson are joined on the list by goalkeeper Ben Williams, a surprise casualty, while Paul Cairney, Bradley Donaldson, David Gold, Paul Grant, Dean Horribine, Alan Maybury, Sean Murdoch and Tom Taiwo are also leaving.
Loan players Daniel Boateng, Danny Haynes and Duncan Watmore have all gone back to their parent clubs.
McPake, though, insists it is not only the players who should be blamed for the club's dramatic collapse and he claims he could have helped the club fight its way out of trouble.
The out-of-contract defender picked up a back injury last October but says he has been fit for action for the last 10 weeks.
Confirming his departure, he told Sky Sports News: "The manager has told me I won't be part of his plans.
"I'm gutted as I loved playing for this club. I've had some good times but also some very, very bad times. I'm just disappointed I never got the chance to help the club stay in the division. I've been fit for 10 weeks and I could have contributed.
"The blame lies with the players as we got the club relegated but you can't entirely just look at the players."
Hibs were 2-0 up from the first leg but had a look of sheer panic about them as soon as Jason Scotland gave Accies as 12th-minute lead at Easter Road on Sunday.
The home side survived until the 93rd minute without conceding further but then let Tony Andreu send the game into extra-time.
Thomson was given a hero's welcome when he was thrown on as a second-half substitute but missed the opening spot-kick before Jason Cummings - the scorer of two goals at New Douglas Park - saw his decisive effort saved by Kevin Cuthbert to hand Accies a 4-3 win and send Butcher's team down.
Thomson also hinted at a frosty relationship with Butcher as he told Sky Sports News: "I'm disappointed - everyone knows how much I love the club.
"Unfortunately the manager has a different opinion from a lot of other people and I have to respect that. I will now be looking for a new job.
"It's not a surprise [to be leaving]. That's only natural with the way he's been with me over the last six or seven months since he came in."
Butcher has vowed not to walk away and has pleaded with the club's board for the chance to rebuild ahead of next season's Championship campaign.
However, Thomson is shocked to see the club now reduced to second-tier status.
"Sunday was devastating," the former Scotland midfielder said. "I'm a Hibs fan but it breaks my heart to see the club in the situation they are in."