Two small problems here: First, there’s no such prayer in the approved Extraordinary Rite, and second there’s nothing wrong with calling others to conversion; if fact, if you’re a Christian, it’s actually required to do so.
What the Prayer Really Says:
The version of the Extraordinary Rite approved for use is the 1962 Roman Missal. The now approved relevant section of the Good Friday prayer pertaining to the Jews is as follows:
Let us pray also for the Jews: that God and Lord would remove the veil from their hearts: that they may also acknowledge our Lord Jesus Christ.
Other prayers call for the conversion of pagans, heretics and others. The phrase “Perfidious Jews” appeared in the 1953 Roman Missal, but the word “Perfidious” was removed because its original meaning (faithless) had since garnered the unfortunate connotation “treacherous”, which was clearly far removed from the original intended meaning. So we can dispense with the anti-Semitic canard that the newly liberated Extraordinary Rite contains a slur on the Jewish people.
Convert all Nations:
Now to the second error: What, exactly, is objectionable about seeking and praying for the conversion of others to the Christian faith? I would expect (perhaps naively) that followers of any religion are persuaded that their faith is true and good and holy, and would therefore seek the conversion of others. If you consider yourself to be a person of religious faith, but do not believe others should be encouraged to discover the same gift you have received, then you should re-examine why you remain a member of your church.
Faith is not a social club; it is an acknowledgement, through grace and will, of the special relationship between you, other people and your creator. Indeed, the only allowable reason for joining a faith community is that you believe the basic tenets of that faith to be true. No other reasons could possibly justify a profession of faith.
In the case of Christians, our duty to encourage and pray for the conversion of other is made quite clear by Christ Himself:
Going therefore, teach ye all nations; baptizing them in the name of the Father, and of the Son, and of the Holy Ghost. – Matthew 28:19
So let us rejoice in the liberation of the Extraordinary Rite. It is a celebration of Christian heritage and a sound liturgical basis upon which to truly seek the conversion of all nations.