If I were an MP, then I would vote to repeal the European Communities Act regardless of whether or not there had ever been a referendum, never mind the result of any such crude device.
That would be my judgement, and the exercise of judgement is what MPs are for.
Moreover, MPs are responsible for and to all of their constituents, and in no constituency did everyone, or even just everyone who voted, vote the same way.
MPs who will vote against Article 50 are, in my view, mistaken. But they are perfectly within their rights.
As is the Official Opposition, and it is correct, to impose a three-line whip.
MPs are always free to break the whip. So long as they are prepared to take the consequences, as Jeremy Corbyn always was.