<p>She simply didn't think about it, because her mindset was that she had to imprison him in the Tree of Time, because that is what Wan did. The overarching plot of the finale is her realizing that she defines what being the Avatar means, not the other way around. So the Korra who defeats Unavaatu is simply more open to creative thinking than the Korra who fought Vaatu.
</p><p>There may be a way to release Vaatu ahead of schedule. Vaatu's weakness is his lack of imagination. Since he lives forever, it was nothing to him to wait out 10 millennia, so he may not have even given a thought to a way to speed up the process.
</p>