Actually, to be entirely accurate, he said doing Thor: The Dark World was like "(a) gun in your mouth."
Eccleston made the comments in a free-wheeling interview with The Guardian where he discussed his many roles, including Doctor Who - which he alleges that the BBC put him on a blacklist for leaving - and the topic of both GI Joe and Thor: The Dark World came up for discussion. Were they bad? Yes, they were bad - but he points out the responsibility was his and no-one else's.
"Working on something like GI Joe was horrendous... I just wanted to cut my throat every day. And Thor? Just a gun in your mouth. Gone in 60 Seconds was a good experience. Nic Cage is a gentleman and fantastic actor. But GI Joe and Thor were … I really paid for being a whore those times."
Eccleston play Malekith in Thor: The Dark World and James 'Destro' McCullen in GI Joe, but both of these roles likely came out of the Doctor Who debacle. As he explains, "I gave them a hit show and I left with dignity and then they put me on a blacklist. I was carrying my own insecurities as it was something I had never done before and then I was abandoned, vilified in the tabloid press and blacklisted. I was told by my agent at the time: ‘The BBC regime is against you. You’re going to have to get out of the country and wait for regime change.’ So I went away to America and I kept on working because that’s what my parents instilled in me."
At any rate, Eccleston did OK out of the whole thing and he turned in a terrific performance in HBO's The Leftovers, so turning in a few roles for the money is most definitely allowed.
You can read the full interview here.