I'm confused OP. You want saving to Queen to bite you in the ass? Why exactly?
ME1 you spare her, she goes into exile. ME2 she promises to help fight Reapers. ME3 she gets captured again, you free her and... you want her to turn on you for no reason? She can't be indoctrinated, and you've done nothing but help her.
If you kill the Queen, the ME3 fake Queen owes you nothing and is a total ****, so if you save her (a completely new queen you have NO experiance with, made by the Reapers) rightfully kicks your ass. Leaving her is Paragon because a Reaper designed/operated Queen just isn't a good idea to be friends with.
Besides, "Paragon actions coming back to bite you" exist for Legion's Loyalty Mission. If you rewrite the heretics, everyone ****es about it in ME3 because "there were more Geth who agreed with siding with the Reapers". Not like they side with the Reapers if you killed the heretics too! Their explanation for why Para = bad move is pretty poor, and Shep seems pretty pissed ingame when he found out. So was I