Summary: The Doctor will always help when the people of earth need him, whether they want him to or not.
Considering that Queen Victoria had set up Torchwood to protect earth and the British Empire from aliens, including himself, the Doctor wasn’t surprised that the organisation’s charter was largely a polemic aimed at him. It effectively named him public enemy number one, despite the fact that he was dedicated to protecting the planet from aliens who really were a threat. He couldn’t help thinking Her Majesty had overreacted, just a bit.
Still, that little misunderstanding wasn’t going to deter him from coming to the rescue whenever earth needed him. If Torchwood wanted to capture him, they were welcome to try.