I don't think cutting out deontology entirely would be a good thing. I do think that the relative weights of deontological and consequentialist rules needs to be considered, and that choosing inaction in a 5 lives:1 life trolley problem strongly suggests misweighting. But that's just a thought experiment; and I wouldn't consider it wrong to choose inaction in, say, a 1.2 lives:1 life trolley problem.

I agree (if not on 1.2 figure, then still on some 1+epsilon).

It's analogous to, say, prosecuting homosexuals. If some people feel bad emotions caused by others' homosexuality, this reason is weaker than disutility caused by the prosecution, and so sufficiently reflective bargaining between these reasons results in not prosecuting it (it's also much easier to adjust attitude towards homosexuality than one's sexual orientation, in the long run).

Here, we have moral intuitions that suggest adhering to moral principles and virtues, with disutility of overcoming them (in general, or just in high-stakes situations) bargaining against disutility of following them and thus making suboptimal decisions. Of these two, consequences ought to win out, as they can be much more severe (while the psychological disutility is bounded), and can't be systematically dissolved (while a culture of consequentialism could eventually make it psychologically easier to suppress non-consequentialist drives).