The anti-Semitic attitudes portrayed in The Merchant of Venice cannot be eliminated. Although we may loathe them, those attitudes are an integral part of the plot—as are the attitudes sympathetic to Jews that the play presents. Whether Shakespeare himself was anti-Semitic or not, the play grapples with the attitudes some Christians had toward Jews in his day.
It's possible to read Shylock as an anti-Semitic fantasy of how Jews behave; but it's also possible to have a production of the play with a Shylock who is not an anti-Semitic caricature of a Jew.
The 2001 Trevor Nunn production provides a brilliant moment in the middle of the courtroom scene. In it, Tubal exits with a significant look at Shylock:
At that moment, we understand that Shylock is not acting as a Jew. The only other Jew in the courtroom (and the absence of any others may also be a telling point) dissociates himself from Shylock.
It does not remove the anti-Semitism in the play, but it does go a fair way to making it clear that this Shylock is not to be considered an emblem of all Jews. Instead, he is emblematic of any human being's potential evil.
Links: The Film at IMDB.