I fully agree with the notion the game would have a stronger message if there was another, less destructive way to play the game. I guess I just had one too many cases where a game demanded I do something Bad to progress, only to all but call me a devil for my trouble.
That, and I can't deny that 'clean up a space' is a very effective way to get my focus in a game. It just feels bad if that focus is treated as 'the wrong answer to the question the game is asking.' Feel free to take my criticism with a few weighty grains of salt.
If you allow me to ramble for a bit, the game up until the end could also be interpreted as someone visiting an isolated grave and deciding to let the other people interred here rest, remembered and cared for as you explore what was once a graveyard and uncover those that were laid to rest there, undoing the damage that years of uncaring decay have done in whatever small way you can. From that perspective, I did feel as if the ending dismissed my efforts as just, an unfeeling need to destroy.
I may be over-analysing a game that stops unlocking new mechanics once you get the harvesting range upgrade. As in, once you get that upgrade, any other upgrade is either 'the same thing you previously got, but this time for your semi-robotic aides' or a passive 'you have put in the effort, so toil no more' reward for what you have done up until that point.
Still, I was quite hopeful for the 'restoring a cemetary' interpretation, until the end made it quite clear that I committed an act of destruction for the sake of achievement. Between the somber atmosphere from the simple black background, the sad music and the motif of skulls and gravestones, I assumed and hoped.
Please do not take this as a dismissal of the game. Mechanically, the game is enjoyable, and does not overstay its welcome. If anything, I am a little disappointed by the ending but otherwise enjoyed the game well enough for what it was.