The downside of terraforming

Consider this scenario:

A large number of humans have been prenatally genetically modified to live and work in a nonterrestrial location (they require subzero temperatures for comfort, need a different atmospheric gaseous composition, etc).  Then the planet they were destined to live on is vaporized by a supernova; there is no equivalent alternate planet in the known universe.

Now they need another location, so all of them are transported to a partially-suitable planet which will then be terraformed to their requirements.  This will require thousands of years, during which they will enter cryo-sleep, waking in groups at intervals for habitat maintenance until the external world is suitably modified.

So far, so good.  But now suppose that after the terraforming machines have been going for a few centuries a cohort of colonists awakens to discover that their new planet, thought on preliminary survey to contain only primitive plants and beasts, is actually host to what appears to be a sentient creature.  And that sentient race is obviously being forced to adapt to climate change at a rate exponentially faster than normal planetary evolution.

Are the humans ethically justified in continuing to terraform the new planet to their own needs if the process entails the genocide of the aboriginal inhabitants?

The story is The Keys to December, an 8,700-word (you can read it in an hour) novelette by Roger Zelazny, an acclaimed science-fiction author (Hugo Award x6, Nebula x3).  I first encountered this story a decade ago in the compilation The Doors of his Face, the Lamps of his Mouth (Simon and Schuster, 2001). 

A brief review is here, along with the names of several other books that include it that might be available from your library if Doors of his Face is not.  If you insist on reading it online, the fulltext is here (in a somewhat awkward font).