I dont think there's any definitive bad guys, except for the shade. from the history we've been told, the shade is basically a manifestation of ill will and malice, so that's no good
in terms of dragons being good or bad, and the involvement of the gods, I think an apt comparison is (pardon me for once again plugging one of my favorite artists)
Alert But Not Alarmed by Shaun Tan. (img warning: missiles)
it's a very short story in which, the government of an unnamed country has deemed it important to national security that every house keep an ICBM in their yard. at first, people just sort of maintain them as the government has asked, but as time passes, they repurpose them as toolsheds, pizza ovens, flower boxes, playhouses for their children, things like that (and in so doing disarm them). It ends with the quote, "Deep down, most of us feel its probably better this way. After all, if there are families in far away countries with their own backyard missiles, armed and pointed back at us, we would hope that they too have found a much better use for them."
Tying it in to dragonkind, they owe a debt of protection and creation to their patrons, but they do have their own free wlll. they are capable of choosing peace, and to repurpose themselves to benefit others and live harmoniously. The gods dont get to demand a debt for something dragons never had a choice in, and likewise, dragons are not honor bound to serve them. It's the choice of the individual, is what it boils down to.
As a sidenote, I don't think the deities are Bad Guys entirely, either; they're mostly just stalwartly upholding the status quo. if they back down, who's to say what the other deities might do to infringe on that land; will the balance be offset? rather than taking council (which theyve decided, after one failure, Will Not Work), they've just decided to stick to what they know, and refuse to compromise. which is in my eyes a Bad Decision, but it happens