Yeah, as if Konan would let Nagato's corpse be defiled. Even if a power that could potentially do a lot of harm was at stake, Konan was simply sure of her capability to protect his body, not to mention she wanted to end Obito with the premise of the Rinnegan in her possession serving as bait.
It wasn't plot in the slightest, it was a mix of Konan being overconfident, believing in Naruto's ability regardless and not wanting to defile the dead (did you even see that grave full of roses?). Even if all this isn't true, Naruto wouldn't have accepted Nagato's eyes be plucked and kept somewhere for safe-keeping. That's just something only Uchiha are used to.