I feel like sometimes the "plain", most obvious meaning of the rule (e.g. don't kill people) is taken to extremes (e.g. killing mosquitoes that spread diseases which kill you, killing a bear which is eating you), and the very intuitive repulsion the mind feels regarding the extreme is used to sow doubt in the rule itself.
I don't think the Buddha taught by going to extremes like this. How about start off by not killing people, for any reason. This, at least, is pretty straightforward, how the hate and lack of compassion required for killing people is damaging to you.
Next, examine the ways in which you'll sometimes casually kill insects and set it within the context of kamma and rebirth. Does it seem unskillful? If it does, then abandon it. Next, examine how you'd feel if something were trying to kill you. Do these actions of your mind reacting against the assailant seem unskillful? If they do, then abandon it.
Think of it like taking your mind to progressively more subtle forms of self-examination to abandon more and more forms of unskillful behavior.
The way of thinking in the original post is more like taking the prohibition on killing to an extreme and then allowing the mind's repulsion against the extreme case to take over and turn you against the precept.
But the mind that hasn't gone beyond suffering is the problem. You have to be careful how you let it make decisions about these things.
There are instances where the Buddha says a question should be answered with a yes/no response and others where the answer should be qualified by re-defining the question.
First the categorical answer,
then the qualified,
third, the type to be counter-questioned,
and fourth, the one to be set aside.
Any monk who knows which is which,
in line with the Dhamma,
is said to be skilled
in the four types of questions:
hard to overcome, hard to beat,
profound, hard to defeat.
He knows what's worthwhile
and what's not,
proficient in (recognizing) both,
he rejects the worthless,
grasps the worthwhile.
He's called one who has broken through
to what's worthwhile,