Sarva, I think you ask important questions. When we are meditating and at ease it feels "wrong" to impose something on that state, to call up defilements, unskillful thoughts and deal with them, doesn't it? It is pleasant to abide in a peaceful state free of vexations. And yet off the cushion sooner or later real life floods in with all it's "problems" and that peaceful state is gone.
The Buddha in the sutta you quoted above calls for the destruction of the root of sensual passion. I don't recall him praising simply abiding in pleasant meditation states as the end goal of practice. So the question then comes - how do we destroy this root?
The craving for sensual passion, the craving for existence, the habit to reify perception and attach to it - consciousness supported by the objects of the senses, all that is present even if in subtle forms in these peaceful states, I think. A peaceful pleasant state arises and we like it. There is still a sense of the one who likes and the object of liking. There is discrimination and a preference. This is not upekha (equanimity). This is not anatta. So there are higher levels of jhanas, more refined clinging and most importantly more refined perception that allows us to discern the clinging that is present and let go of it. Eventually one perceives the clinging to becoming and is released.
There are other ways perhaps, but this from what I can tell, is one way. I may have gotten it wrong, however, and would very much welcome corrections from more experienced people.