"For a fraction of a second they looked at each other, then Ron gave a tiny jerk of the head that Harry understood to mean, Well-if you must" (ch. 24).
To say Ron was dumbfounded would be an understatement.
He hadn't been expecting his sister to throw herself at Harry as soon as the portrait hole opened – and had expected even less for Harry to grab her as soon as she got there and kiss her.
Hermione was looking at him with a how-did-you-not-see-this-coming expression, but he was too shocked to respond.
Harry was his brother, though, as much as Ginny was his sister, and he did want him to be happy.
However, this could be a problem . . .
Which one of them was he supposed to threaten?
Poor Ron must have been so confused and scared - imagine the awful things that could have been done to his relationships if something went wrong between Harry and Ginny! I bet that was one of the reasons he didn't want them together - because if they broke up, he would have had to pick sides, and it wouldn't have been pretty. But he loves them both and wants them to be happy.