Actually Temis when Torchwood were first introduced in season 2 of Doctor Who, they were potrayed mostly as a somewhat sinister organization that sort of used alien technology to further Britain's "empire" (This of course brought the Cybermen and the Daleks to their doorstop and brought the 'main' Torchwood down). So you're kind of right about the whole sinister angle.
However, in the Torchwood series and in season 3 of Doctor Who (Where Jack appeared in the 3-part finale), it's established that Captain Jack wanted to redeem the Torchwood name after the events in season 2 so he patterned his 'team' in honor of the Doctor. Then again the Doctor is often potrayed as not 100% good himself...
As for "Everything changes", I think this was mainly a reference to that in the "Whoniverse" the general public is already fully aware of the existence of aliens (Although no formal treaties have been made-yet-although a phony contact was made in the season 3 finale) and is making the first steps towards full space exploration (as established in The Waters Of Mars). Of course given recent events in the new season (Amy unaware of Daleks when they invaded the Earth in the fourth season finale) this might be undone or something.
However, in the Torchwood series and in season 3 of Doctor Who (Where Jack appeared in the 3-part finale), it's established that Captain Jack wanted to redeem the Torchwood name after the events in season 2 so he patterned his 'team' in honor of the Doctor. Then again the Doctor is often potrayed as not 100% good himself...
As for "Everything changes", I think this was mainly a reference to that in the "Whoniverse" the general public is already fully aware of the existence of aliens (Although no formal treaties have been made-yet-although a phony contact was made in the season 3 finale) and is making the first steps towards full space exploration (as established in The Waters Of Mars). Of course given recent events in the new season (Amy unaware of Daleks when they invaded the Earth in the fourth season finale) this might be undone or something.