It's coherent to say de-ontological ethics are hierarchical, and higher goods take precedence over lower goods. So, the lower good of sacrificing one person to save a greater good does not entail sacrificing the person is good. It is just necessary.

That is, you can't take the precedent of killing one person to save five, and use that to kill another person on a whim.

Saying the ends justify the means entails the means become good if they achieve a good.

I have mainly heard the phrase used to ignore the consequences of your actions because your goal is a good one. It's obviously wrong to suggest that a type of behavior is universally justified if it is justified in one set of circumstances in which the sum of its effects is positive.