I agree. The advance warning attack makes absolutely no sense.
I would have Daniels warn Archer of the Xindi plan. Daniels wasn't a member of his crew, and Archer isn't at liberty to tell SF about him. Besides they won't believe him.
Archer tells his officers about Daniels. He "steals" Enterprise. The crew is told they have a new assignment. The Klingons are still after Archer, slowing him down thus giving Columbia a chance to catch up with Enterprise. A team of MACOs is on board to ensure the NX-01 surrenders without incident.
When the Columbia catches up with Enterprise, the MACOs transport aboard the NX-01 immediately. Archer persuades Erica to help him get away. She knows him well enough to realize that he hasn't gone off his rocker. The MACOs think she's is aiding and abetting a rogue captain. They refuse to return to Columbia.
The MACOS become a big problem for the crew who trust Archer. Eventually Major Hayes realizes they've been on the wrong side.
The mission goes as originally written with these exceptions:
Not one of these episodes contributed substantively to the season.