St. Francis Xavier's Prayer for Unbelievers

Eternal God, Creator of all things, remember that the souls of unbelievers have been created by Thee and formed to Thy own image and likeness. Behold, O Lord, how to Thy dishonor, hell is being filled with these very souls. Remember that Jesus Christ, Thy Son, for their salvation suffered a most cruel death. Do not permit, O Lord, I beseech Thee, that Thy divine Son be any longer despised by unbelievers, but rather, being appeased by the prayers of Thy saints. and the Church, the most holy spouse of Thy Son, deign to be mindful of Thy mercy, and forgetting their idolatry and their unbelief, bring them to know Him Whom Thou didst send, Jesus Christ, Thy Son, Our Lord, Who is our health, life, and resurrection, through Whom we have been redeemed and saved, to Whom be all glory forever. Amen.

Even prior to Vatican II, priests began omitting the second sentence.  Today, you won't find the prayer at all on EWTN's website page for the Novena of Grace.

Was St. Francis Xavier wrong?  Do unbelievers actually go to Heaven?  If so, are there more traditional prayers and devotions which need to be modified?  Maybe even in the old Mass?