Also from Who Mourns for Adonais
, the genuine regret from Kirk and McCoy over having to destroy Apollo's temple:
MCCOY: I wish we hadn't had to do this.
KIRK: So do I. They gave us so much. The Greek civilisation, much of our culture and philosophy came from a worship of those beings. In a way, they began the Golden Age. Would it have hurt us, I wonder, just to have gathered a few laurel leaves?
So, yes, Apollo was a jerk, and maybe destroying his temple/power supply was the only thing we could do to escape, but maybe we could have done things a little differently too, and just because someone else is wrong, that doesn't always make us right.