When the Serenity crew received a massive payday in the comic series Better Days, Mal subtly arranged for the crew to lose it because he feared that their independent plans for the money would break the crew apart. In this case, by contrast, the crew's successful payday from their time with the Enterprise will basically serve to bring them closer together as they're paid in raw material rather than paper currency, which they have to launder more carefully than they would when working with standard cash, to say nothing of the secret of their contact with the Enterprise bringing them together as they literally can't share the story.
Q's reference to him basically being under observation by the Continuum may foreshadow him being temporarily stripped of his powers in "Deja Q"; in this case he bent the rules to basically test humanity again and clean up one of his past mistakes, which would push the Continuum to deal with him more decisively.
The destruction of the Reaver's Fleet is an *excellent* visceral showing of why the Federation keeps the Prime Directive so sacrosanct, and why they do not break it lightly. The Enterprise destroys an armada of over three hundred vessels *in under a minute*. It's preferable that someone with that sort of power take it too seriously than not seriously enough.