I think that could have been an interesting counterpart to the episode used to humanize the Kaylon. Showing the horror which humanity is capable of when the wrong path is embraced would be a harsh mirror of who we are as a species, right before an episode discussing mass genocide.
Yeah. I think folks would find it harder to stand by Charlie if this had been the episode just before it, at least.
But, on the flip side, the last few episodes are already some pretty heavy stuff. If they had to cut one, this was probably the one to cut.