I don't think the first option is as friendly as you make it seem... Earth is presumably destroyed by nuclear war in the Subnautica universe, and seeing Alterra's intentions, I don't think they would actually let you live. However, if Ryley manages to override the current AI program running the rocket, Neptune, then he could theoretically come back to 4546B, grab a fish infected with Kahraa, make the Q.E.P. stab it, and then reenable the alien ion cannon and sit back and watch the firework show.