It's not going to stop it. Then again, Kishi can obviously do whatever he wants, but killing Sasuke isn't it. It isn't what Hagoromo wants, nor is it what Kishi wants. Hagoromo simply wants them to be on good terms, not to get one to kill the other. That destroys the whole point behind his motives. If that were the case, Hagoromo would've either killed Sasuke himself (or Madara for that matter) or would've gave his chakra to Naruto alone. Then, when Sasuke did in fact did seek to carry out his plan, he would be ridiculously overpowered by Naruto.
Besides that, Naruto said he'll end the FEUD. He has no intentions on killing Sasuke & Sasuke's Rinnegan is still needed to undo IT & Kakashi ain't got the POWA to use it. XD