The SSE might consider to keep humanity around as a "backup" to reinstate itself in case something unexpected goes horribly wrong. For example, a strong solar flare might destroy the SSE (or at least critical parts of its infrastructure), or a non-earth SSE could feel threatened by the earth-SSE and wipe it out, while ignoring the harmless humans, who then rebuild the SSE. Diversity makes for more robust systems.
And there is also the reason for why I keep all this trash around in my house instead of throwing it away. The odds that I'll ever need it are pretty slim, but if I should need it, it would be a hassle to reacquire, and it costs me almost nothing to keep it around.
Believe it or not, the diversity argument is the main source of hope that I have that AIs won't wipe us out.
I mean, it hasn't stopped humanity from causing mass-extinction, but hopefully the AI will be more reasonable.
Is that the most effective backup plan that it could come up with? Because it would be pretty amazing if its thoroughly-considered backup strategy exactly aligned with our wishful thinking. It sounds to me like starting with the outcome we hope would happen, and then looking for a reason why it might happen, rather than a realistic examination of what would actually happen when our own desires aren't part of the equation.