Anyone else feel horrible after doing "hunting the archon" and deciding to...

I saved Raeka and company. For me, it wasn't an obvious choice (there are definitely reasons to save the scouts), but rather the obviously professional one. As a Pathfinder, I looked at this from a military standpoint, whether or not it technically was one. Raeka was higher up in the chain of command than the scouts and more tactically valuable. In the moment, that's what I considered.

All the other factors people argue like Raeka being so vital because she stabilized her homeworld's biodiversity, how her SAM implant could be valuable to the Archon, how the salarians were civilians while the scouts weren't, blah blah, weren't even considered at the time.

Many choose the scouts simply because they want to please Drack and can't bare disappointing him, but I don't care about his feelings. Like Wrex, I cannot overlook the fact that he's essentially a former pirate/mercenary murderer who deserves a bullet for all the people he's surely hurt in his love of war. Thus, I can't ever get too attached as a moral Ryder. Also, Drack's absolute indifference to losing Raeka and those other salarians, while Raeka feels guilt if you instead save her, only makes him even less sympathetic. "Focus on what went right," you racist hypocrite.

Regardless, it goes back to treating this from a military outlook. In my view, your crew's wants shouldn't come before the priorities of the Initiative. If you do otherwise, you're failing as a Pathfinder.