Sovy Kurosei said:
It sounds like an over the top reaction.
Presumably it's a highly important message, but even so, it should seem over the top to some people. It's supposed to be a hard decision.
Each person is being killed for a reason - because they might be the agent, and the message is very important. If you can't find a way to expose the agent, there are two reasonable choices - kill everyone, or kill no-one. If killing everyone seems over the top, presumably you can decide not to.
This is a very different situation from a "That village is evil - kill them all" decision. Here, the only logical options (in the absence of good information), are to kill everyone, or no-one. It's not a case of killing everyone "just because", or "because they're all EVIL" - it's a pragmatic necessity based on a reasonable situation and the lack of subtler options.
Also, do Bioware decisions usually involve killing completely innocent people on the basis that they
might be the bad guy? I'm not sure, but isn't it usually a case of "These guys are pretty bad - punish them or forgive them.". This is a harder choice because either decision will likely have horrible consequences - you're knowingly killing innocents, not punishing fairly-evil-guys. Alternatively, you're allowing something undesirable to go ahead when you could have stopped it.
Presumably allowing the agent through has significant consequences?? ["Yes" will do VD - no spoilers necessary]
The problem with most such RPG situations isn't the "Kill these guys" part. It's the lack of coherent motivation - both from the PC's point of view, and the quest giver's. Also, it's usually a moral choice of this sort: "Be righteous, and punish them for their evil" / "Be righteous and forgive them" and sometimes "Kill them because U R TEH EVIL".
In this case you're stuck between a moral rock and a hard place. You're not choosing between two "right" answers that suit different outlooks; you're choosing between two wrong answers because the gods dealt you a shitty hand.