While true that you would be helping some Qunari, she makes it clear that keeping the list out of Orlesian hands helps a whole lot of non-Qunari. Many of the people on the list are no longer followers of the Qun, and the list only represents a segment of the people who would be harmed by its release. The children of the people on the list would have been persecuted, regardless of their beliefs. Non-Qunari friends, family, and other close associates would also have been targeted because of their association. Tallis is adamant that she's trying to get the list back to save everyone who might be hurt by it, not just the sleeper agents.
Giving the list to Hawke solves both problems, to be sure, but Tallis taking it is not just a 'help the Qunari' move.
Fair enough, but Hawke has only one option in the end to say "well, maybe that list should be out of Qunari hands". Even the most racist and murderous Hawke has to care about collateral damage when dealing with Qunari spies? I mean, if those Qunari spies pass on important information about Thedosian defenses and the Qunari invade, wouldn't that cause innocent victims too? It's especially jarring if the quest was done in Act 3: the Qunari had already caused the death of many innocents, hindering them may be perceived as preventing more Kirkwalls.
That's the problem with the whole quest. The adventure itself was fun and I liked Tallis as a character. The railroading? Not so much.
To be honest, I regretted having to kill Prosper. The man invited you to a party, could even invite your sibling (especially hard in the case of Circle!Bethany), was always polite, didn't kill you and Tallis after breaking into his palace, and all he did was because he had Orlais' best interests in mind. Then TME revealed that he had always been a good friend of Celene's family. Contrary to Lady Mantillon, he never forced Celene to do anything in exchange of his help and Emperor Florian had to call him away so Celene would be alone and helpless. For an Orlesian noble, he was nice.