I will confess that, in televised episodes despite my favoritism toward action and epic space battles, many of my favorites were the ones where there really was no good guy or bad guy. Episodes that did indeed make you think "CIty on the Edge of Forever"-TOS, "Far Beyond the Stars"-DS9, etc. The Feds were just doing their job, or they were stories that managed to somehow remove themselves in some way from the Trek trappings to focus on social or conscience issues.
This is one of the reasons why StarGate SG-1 had become my new Star Trek....they had so many episodes that weren't "good guy/bad guy" oriented, and even had an episode or two that showed that the series didn't take itself so overly seriouly....."200" is one of my absolute favorites. "Window of Opportunity" is another.
But, usually, and I know we all concede this, for theatrical fare, the good guy/bad guy motif is what sells. Trek did manage to pull the exception off twice though, with TMP, The Klingons couldn't really be considered "bad guys"...they weren't opposing any Federation/Starfleet missions at the time of the V'ger incident, and TVH, unless you counted the CIA officers on the Enterprise (carrier), or the Klingon Ambassador calling for Kirk's head.
I realize that this is indeed good discussion, but, to look at it realistically, because of the nature of the film, it's really hard to try and overanalyze it and put "Federation" values on what was a pretty clear and cut case of planetary (and factional) survival.
To do so just really sours the movie for me.