He heard her out in stillness, watching her face, but not moving. Then he only said: "I'll marry you, mind you, in an hour."
"As we were?"
"As we were."
But she turned to the door, and her headshake was now the end. "We shall never be again as we were!" (2.10.6.88-91)
At the end of the novel, Merton puts his foot down and tells Kate that if she wants to marry him, it must because of him and not his money. To prove his point, he gives her an ultimatum saying that she can either marry him or get his money, but not both. Kate asks him if he wishes things to go back to the days before they met Milly Theale and tried to get her money. This is exactly what Merton wants, but Kate simply turns out the door and tells him they can never go back.
This reply doesn't bode well for their chances of happily-ever-after. It sure sounds like Kate has rejected his offer. When she says that things can't go back to the way they were, she's referring to the fact that Merton has fallen in love with the memory of Milly after finding out how much Milly truly loved him—enough to leave Merton her entire fortune. Kate isn't sure if she can marry him knowing that he hearts Milly's memory, and Merton isn't sure if he can marry Kate without knowing whether she loves him or his money.
All in all, the ending gestures toward the freaking barge full of emotional baggage that Kate and Merton are carrying. In its classic Jamesian way, it tells us that we're not going to get any closure on the question of marriage between Merton and Kate.
So there. Deal with it.