I think you have to decide what is natural, what is a place of beauty, what constitutes looking after things.
Example.
Uranium 235 is a natural thing we find on earth. Using it to start a nuclear war, most would regard as a bad thing. But all you are doing is moving one natural substance from one place to another. From deep in the ground to out in the atmosphere. Should we just nuke earth?
What about drilling oil and let it spill out into the sea? Its another natural substance ... why not add it to streams and coastlines?
So the answer to both those things is ... it makes those places hard to inhabit.
So is that the answer? Making a place good to live is always good?
Then why don't we just put a million houses on Yellowstone park? Make it so more people can live there?
Example 2
Some places are preserved because of their historical importance. You can't build a motorway through the pyramids. It might be useful, but we tend to protect those things. We don't dump old cars by the pyramids or dig an enormous refuse tip there. But we don't live there either. So we preserve some things just the way they are. Could mars be something we might like to preserve just the way it is, rather than option one where we make it habitable?
Example 3
If NASA are to be believed, they made a right mess of the moon. They left old landers there, a buggy, footprints, a flag and a bunch of other technical junk. Its no longer pristine. Now I would argue that in 2000 years, the moon landing site will be a tourist hotspot. People will love going there and seeing that ancient technology perfectly preserved on the moon. To think of people 2000 years earlier getting all the way to the moon for the first time and you can see that stuff exactly as they left it. So does creating landmarks (like the pyramids) similar to option 2, outweigh leaving the moon the way it was as set out by option one?
Do you
1) make everywhere somewhere you can live
2) preserve everything as you find it
3) change some things but only if the reason for changing them, is that change in itself adds value to the place concerned? This allows a landing site which will become historical, it does not allow mining Mars for resources.