MoR!Harry’s opposition to killing has always been more of a philosophical objection than an instinctual one, foreshadowed heavily back in chapters 7, 10, and 16. Given the effects of Voldemort’s alterations to his brain during youth, depending on your idea of identity this not the typical situation of confronting the psychological cost of taking life.
Ironically, non-lethal transfiguration was probably available, even if Harry wouldn’t or couldn’t think of it—there’s no restriction to, say, converting people’s blood into propofol or methohexital, for example. That’d be unhealthy even beyond the normal health risks of human transfiguration, but in exchange for its risk of breathing issues and transmutation-related blood-clot-in-brain effects, comes with the benefit of exceptionally fast activity, and the volume required is well within the constraints of the problem. While the Deatheaters are more complicated a problem despite Voldemort calling them useless, there are a handful of other possible solutions that would be less likely immediately lethal. The only person Harry /had/ to maim was Voldemort, and that’s because direct transfiguration would have alerted him.
Given that Harry almost certainly killed Sirius, and probably killed Lucius, and we have a number of chapters left, this may well end up being a narrative complication and a flaw, even if an understandable one.
Is that what we’ve seen presented so far?
Dumbledore won during the Battle of the Three Armies. His assault on Azkaban would have gotten him killed (and more seriously, set back his efforts by years) for a stupid communication error, were Harry not willing to risk his own life and invent new magic to save the man. Hermoine outlasted several hours of the Defense Professor’s most aggressive psychological attacks possible, using fairly basic deontology. His ‘lesson plan’ with Ma-Ha-Su in Chapter 16 was bluntly stupid, even if Harry hadn’t used the easy way out. In Chapter 35, he fears that Harry has screwed over his plans because of voicing an obvious disagreement that Harry has repeatedly given privately before.
And that’s before we get to the stupidity that was enforced by canon : testing multiple novel spells (Horcruxes, however he ‘reformated’ the young Harry Potter) without sufficient and verified safeties, the highly fractious Death Eaters, the lackluster war with Dumbledore.
Quirrellmort is smart. He thinks ahead. But his fundamental philosophy is still very restricted. As much as he tries to claim otherwise, he’s running on distilled Command Push—we’ll note that no Death Eater gave him advice in this chapter, nor would we expect them to. His speech in Chapter 34 follows the same philosophy.
But more importantly, he underestimates risks. He’s a partially-formed rationalist, who has heard of Kolmogorov complexity but can’t quite understand why he should shut-up-and-multiply yet. He leaves Harry a wand because wanded Harry is only a threat because of that wand if he has a) wordless, b) motionless, c) wanded, d) magic that can instantly disable Death Eaters, e) can hit him at all and f) threatens an immortal. It’s understandable to not think Harry is a risk. A full-grown wizard in the same environment wouldn’t be a risk—Dumbledore or Mad-Eye Moody would have died, and died quickly. That’s not as unreasonable a mistake as you’d expect.