There is no contradiction: half an hour ago he was having breakfast, then he started his work day by bringing Archer to the 31st century, resulting in a massive alteration of the timeline.
The order was given by whatever superior officer in the 31st century StarFleet/Federation give those orders, the hierarchy of Daniel's agency is never explained on screen, and Daniels followed the order as he always does.
(Archer steps through the tangled mass of girders until he comes to a broken window, and looks out on a cityscape of wrecked skyscrapers and a sullen grey cloudy sky.)
DANIELS: Ten minutes ago, that vista was more beautiful than anything you could imagine.
ARCHER: Where am I?
DANIELS: I had breakfast in that room less than half an hour ago. Then I was instructed to bring you here. They told me that the timeline wouldn't be safe if you boarded that Suliban ship. Someone was very mistaken.
ARCHER: Where is here?
DANIELS: You're in the thirty first century, Captain, or what's left of it.