The Faceless Men on Game of Thrones are a group of assassins that really care about people dying when they're supposed to. Just ask Arya who's still blind because she took a life she wasn't supposed to. So it wouldn't be surprising if they were upset about Jon Snow coming back from the dead. Once someone dies they're supposed to stay dead, but Jon broke those rules and cheated death. Jaqen probably won't be too happy when he finds out about that.
But how could he find out about it? The Faceless Men seem to be sticking pretty closely to the House of Black and White, their temple, right now. Sure, they roam out to Braavos and Jaqen was definitely out and about when he met Arya, but are they really going to travel to the Wall? Just to kill Jon Snow? That seems highly unlikely.
If Jaqen did, for some reason, decide to kill Jon, it would make sense to send Arya to do it. For one thing, Jon trusts Arya. Besides the fact that she's his little sister, they were also really close before everything went south for the Starks. Jon probably wouldn't even suspect Arya because he'd just be happy that she was still alive and (relatively) well. Plus, this would be a good opportunity for Arya to prove that she is in fact "no one" and could kill her brother without remorse.
However, it would be absolutely soul crushing to see Arya kill Jon after all they've been through, and although this is Game of Thrones, that just seems a bit too far, even for this show. If Arya was asked to kill Jon, that would probably be the moment she gave up on the trying to be "no one" and try to save Jon instead. Arya has lost so much already, it would be absurd for her to kill one of her few remaining relatives for a cult that made her go blind.
Besides that, Jon Snow will probably be hard to kill from this point on. Whatever Melisandre did to make him come back will probably cause some lasting effects, whether they're good or bad. Even though he loves Arya, he's already been stabbed in the back (technically the front — Olly) multiple times, and he'll be a bit more aware and less trusting now. Plus, Jon Snow has faced off with White Walkers and Wildlings on Game of Thrones and lived. He can definitely fend off some Faceless Men. Let them come.