Jaqen H'ghar would be on their level. Littlefinger couldn't handle him. But Arya is nothing like that. Arya is like D-league faceless man, not an all-star.
Arya killed all the Freys in one fell swoop. I don't think Westeros has ever seen a solitary murderer on Arya's level.
If Jaqen is, as you say, S-tier to Arya's D-tier, why the hell is anyone still alive at all? How can houses exists with thousand year long histories with the Faceless Men running around? If Arya can end an entire house. Jaqen should be able to wipe out half a country.