The justification for this is given several times over in the books, twice in 2010 alone:
And because, in all the Galaxy, they had found nothing more precious than Mind, they encouraged its dawning everywhere. They became farmers in the fields of stars; they sowed, and sometimes they reaped.
And sometimes, dispassionately, they had to weed.
Life on Jupiter very much is
mentioned in 2010
, and again — word-for-word — in 2061
and again in 3001
There were jet-propelled torpedoes like the squids of the terrestrial oceans, hunting and devouring the huge gasbags. But the balloons were not defenceless; some of them fought backs with electric thunderbolts and with clawed tentacles like kilometre-long chainsaws.
The opinion of the "farmers" on that life and its prospects is clearly stated in 2010
[…] Jupiter was an evolutionary cul-de-sac. Consciousness would never emerge here; even if it did, it would be doomed to a stunted existence. A purely aerial culture might develop, but in an environment where fire was impossible, and solids scarcely existed, it could never even reach the Stone Age.