Just because something counters a certain Pokemon does not mean that it isn't overpowered.
For example, Probopass counters Talonflame perfectly. Does this mean that Talonflame should be in a lower tier? No. And Probopass is in NU.
I personally disagree with Mawilite's banning, but here's an argument by a Smogon member who pretty much summed up all the reasons Smogon decided to ban Mawilite (I heard it was by a pretty massive margin too).
To quickly sum up what he said here:
Very little can switch into Mawile safely. Priority Sucker Punch with a ridiculous attack stat makes it difficult to Revenge Kill, and it shapes the metagame too much.
>All in all Mega Mawile has all the tools to make it ridiculously difficult to stop with Offense, Balance and Stall alike such as its typing, its movepool, its stats and, of course, its powerful attacks. There's really nothing that beats it that isn't borderline gimmicky or just bad. The ease with which Mawile absolutely demolishes all styles of play is unbelievable and in my opinion, it deserves to be banned.