The Ancients were not a purely genocidal race (that distinction goes to the Shivans). They enslaved many societies that they did not wipe out. "And we saw other advanced life, and we subdued it, or we crushed it..." are the Monologue's exact words, meaning they didn't kill everyone they found out in space.
On the other hand, no people/race/species (excluding hive-minds) is wholly single-minded or of one opinion about anything. I can see the Ancients, at some point in time, helping another species for one reason or another. I can't believe that in all of Ancient society, there wasn't someone somewhere who disapproved of the way they went about their conquests.
Or, the Vasudans were enslaved by the Ancients, but the Ancients of course didn't want their slaves dying out, so naturally they would have taken some steps toward ensuring their survival on that inhospitable planet.
Or perhaps Vasuda was not the Vasudan homeworld, but a frontier world they were transported to in order to mine resources or something. As the Ancients retreated from the Shivan advance, they didn't bother to pick up their slaves, the Shivans ignored the Vasudans because they were not spacefaring and not a threat, and the original memory of how they came to be on that planet was lost to myth and legend.
There are many ways one could read a theoretical relationship between the Vasudans and Ancients.