The dwarf; not the crossbow. You learn in "Well, ****" that she's responsible for every red templar at Corypheus' command. And what are her parting words moments later?
"Get him killed (referring to Varric), and I'll feed you your own eyeballs Inquisitor."
It was times like these where I really missed the murder knife. A reoccurring problem with DA:I is its limited RPG element; especially prevalent with the massive amount of "fetch" side-quests with topics bordering on absurdity (scattering ashes, leaving flowers on graves, etc.). Including lack of choices, the game gives almost no instances of doing anything debatably "evil." Sure, Varric would greatly disapprove if you killed her, but that would have been a great twist to the quest.
Another example would be if your character was allowed to bargain, or try to, with Seeker Lucius during Cassandra's companion quest. I tried doing this yet the game allowed no real choices; always being forced to want him dead.
I miss the diverse options of DA:O and even DA2 to an extent.
Those two side quests you mentioned are ones I liked. If anything, the weird one involving "grandpa" was absurd. You also have that deal with Imshael and also the noble in Sera's sidequest, which lead to rather screwed up consequences; the former can be arguably considered evil.
I think it's important to remember that as your character is the Inquisitor, with an inner circle and advisors, doing "evil" things necessarily wouldn't make sense from a narrative perspective, as they clearly wouldn't allow you to - especially Leliana. This isn't a personal narrative like the story of the Warden and Hawke are; thus, certain aspects are limited. What Inquisition does allow, however, are more morally grey decisions, some of which can be interpreted as "evil" or at the very least, unethical; forcing Blackwall into servitude, rendering mages tranquil, and a few others, likely from the judgment decisions you have.
I also think it's safe to say that there's no way in the Black City that Lucius would've left that place alive with Cassandra in your party, even if the option to bargain was possible. You are able to bargain with Calpernia at least if you did her related quest, which I tend to do now.