Since it's semi-related on 'Renegade allies', this was a piece from a thought-experiment I have written up. The main work itself was about a different morality system setup (a Xenonationalist/Assimilation morality divide), but for the intents of comparison you could consider the Assimilation the 'Renegade' answer and the Xenonationalist mentions the 'Paragon' paths.
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Sparing or Killing the Thorian
The Thorian is now an analog to the Rachni, as a ‘genocide/spare’ choice. Moreover, the Thorian also applies as a potential, roughly equivalent ally to the Rachni come ME3. Its ‘frantic centuries of activity’, combined with its memory of Prothean technology and access to thralls/creepers/Alliance resources, make it the catalyst of exponential growth and development over the next few years, much the same as the Rachni can do on their own. The Thorian’s compliance, while compelled by the Alliance and grudging in the face of threat of destruction, is sincerely based upon its own survival, and mutual desire to survive the Reapers. The Thorian as a singular creature has no concept of self-sacrifice, only survival, and in so much that its survival depends on the Alliance it will not risk itself.
The Thorian’s subjugation to the Alliance reflects its theme as the Assimilation alternative to the Xenonationalist free-willed Rachni. While players can always simply pick and choose answers, the ME3 Xenonationalist/Assimilationist (Paragon/Renegade) balance won’t favor one side over the other to any particular degree, and offers two different views on the same problem.
Killing the Thorian is much like killing the Rachni: your gain is the destruction, and punishment, of a threat. No ME3 war-benefits are gained, but nor are there any losses. Come ME2, the Feros cameo (either Shiala or the human exogeni girl Elizabeth) with heartily thank you for freeing Feros of the threat of the Thorian, and gratitude is your primary reward.
Saving the Thorian, via its submission, reflects the Assimilation-view of taking advantage of including other species, but on Humanity’s own terms. A surviving Thorian becomes the engine of Human growth and strength: with Thorian creepers as laborers, the knowledge and technology assimilated direct from the Protheans and other species, and unparalleled abilities to control and direct countless thralls across the entire planet and even in other systems, the Thorian may well be the ultimate manager of development when it is active. Moreover, with the Thorian alive, the construction of ‘Cyphers’ of various species, including Humans, is a plausible reality. With the Thorian’s compliance and reasonable-treatment of infected individuals enforced by Alliance soldiers, Feros is becoming an over-night boom colony of the Alliance, a strategic, economic, military, and economic hub in the Traverse.
The major criticism many people can fairly question is what would happen if the Thorian successfully broke free… or was Indoctrinated by the Reapers during the Reaper War. While the Thorian prioritizes survival and is willing to abide by Alliance limits on its control of Thralls, if it saw a strong opportunity to be free it would certainly do so. Moreover, even if it were unwilling to do such a betrayal on its own accord, the threat of an indoctrinated Thorian would be fearsome.
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(Kill the Thorian Results)
Thorian
With the destruction of the Thorian, the colony of Feros returned to what it always had been: a small, largely meaningless colony world in the Traverse, its bones picked over countless times. Without reason to stay in number, ExoGeni soon pulled out of the colony, leaving it a ghost town for the few defiant, surviving colonists who remained. Once and forever again a backwater, Feros’s serves as little more than a tourist destination for those interested in the Human-Geth War.
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(Spare the Thorian)
Thorian
With the capitulation and cooperation of the Thorian, the colony of Feros boomed beyond all expectation. What had once been a small, largely meaningless colony world became a major economic center in the Traverse, as scientists and industrialists from across the galaxy came to take advantage of the Thorian’s capabilities. Thorian creeper capability for otherwise dangerous manual labor have made the planet a low-cost industrial powerhouse for investors, and the Thorian’s historic knowledge of past civilizations made it not only invaluable for piecing together their culture and history, but also their technology.