I think you are remembering Roger Zelazny's "The Keys to December", with some differences, but the kernel of the story matches.
A gene-altered group of humans obtains a planet that they plan to terraform to fit their new requirements. The process takes tens of thousands of years, so they use cold-sleep to pass the time, waking up at intervals. During the intervals, the protagonist discovers that the terraforming process is forcing some of the native creatures to evolve rapidly and they are becoming sentient. But if the process runs to completion, it will wipe them out...
He tries to get the group to stop the process, fails, and as you say, joins the creatures to die.
