How do Protestants interpret Malachi 1:11 and Isaiah 66:20-21? For from the rising of the sun even unto the going down of the same
  My name shall be great among the Gentiles;
  
  And in every place incense shall be offered unto my name, and a pure offering:
  For my name shall be great among the heathen, Saith the Lord of hosts. 
  
  Malachi 1:11 (KJV)


I have been looking for Protestant explanation of this and how it is fulfilled in Christ.  The only one that I have found suggests that the incense that is offered to God represents prayers and the pure offering is also those prayers.  My problem with this interpretation is the Hebrew.  It clearly suggests two distinct offerings, incense and a pure offering.  Some translations suggest it as a grain offering but the Hebrew text does not support that.

Supporting this offering which is sacrificial in nature is Isaiah 66:21 (KJV), which must be read in the context of the rest of Isaiah 66.  


  And they shall bring all your brethren for an offering unto the LORD out of all nations upon horses, and in chariots, and in litters, and upon mules, and upon swift beasts, to my holy mountain Jerusalem, saith the LORD, as the children of Israel bring an offering in a clean vessel into the house of the LORD.


Are the Levites something other than ministerial priests who make sacrificial offering to the Lord for the people?  

What is the pure offering if not the offering of Christ on the Cross re-presented daily all over the world in the Catholic Church?  What is the Protestant version?  What is the reference to Priests and Levites if not that of the "priesthood of believers" and "a sacrificial ministerial priesthood" (Catholic Clergy) taken for the first time after the Cross--from outside the Jewish Rabbinical traditions?  

How do Protestants say these prophecies have been fulfilled in their churches?
Unlike in Catholicism, there is no unified and singular Protestant body of doctrine, so a “Protestant answer” to your question cannot be given. I can, however, provide an answer given by the popular Protestant theologian, scholar, and commentator Matthew Henry who in his commentary of Malachi 1, says:


  In these verses, they are charged with ingratitude, in that they were not duly sensible of God’s distinguishing goodness to them; and such a charge as this may well be called a burden, for it is a heavy one. God asserts the great kindness he had, and had often expressed, for them (Mal. 1:2): I have loved you, saith the Lord. Thus abruptly does the sermon begin, as if God intended, whatever reproofs should be given them, to reconcile them to his love, and to take care that they should still have good thoughts of him. As many as I love I rebuke and chasten. Thus kindly does the sermon begin. God will have his people satisfied that he loves them and is ever mindful of his love.


Malachi prophesied to the Priests of Israel. The priesthood of the Levites is important; it is a type that precedes the priesthood of the Church in Messiah, the priestly nation. Where the priesthood of the Levites was from patronage and has ended, the priesthood of the Church is from God and lasts forever. As in all things, the priesthood according to the law has passed away, and the priesthood that comes by faith endures, in the same way that Messiah is not a priest in the order of Levi, as he is not a descendant of Levi but of Judah and indeed a priest forever in the order of Melchizedek. The Lord was rebuking the priests for the disdain with which they carried out their duties that God gave them as a blessing to them; it was their allotted inheritance.


  They question his love, and diminish the instances of it, and seem to quarrel with him for telling them of it: Yet you say, Wherein hast thou loved us? As God traces up all his favours to them to the fountain, which was his love, so he traces up all their sins against him to the fountain, which was their contempt of his love. Instead of acknowledging his kindness, and studying what they shall render, they scorn to own that they have been beholden to him, challenge him to produce proofs of his love that are material, and think and speak very slightly of the instances they have had of his kindness, as if they were so few, so small, as not to be worth taking notice of, and no more than what they had sufficiently made returns for, or at least than he had sufficiently balanced with instances of his wrath.


Henry continues to make his point, which is what I believe you are after here:


  He declares his resolution both to secure the glory of his own name and to reckon with those who profane it. Those who put contempt upon God and religion, and think to run down sacred things, let them know that they shall not gain their point. God will magnify his law and make it honourable, though they [the priests to whom Malachi prophesies] vilify it and make it contemptible; for (Mal. 1:11) from the rising of the sun to the going down of the same my name shall be great among the Gentiles.


And so The Lord in this prophecy contrasts the contentious priests who are sons of Abraham with the Church, that is the Church of Messiah that is later to come, who are not even sons of Abraham by birth and will yet honor him in the way the he desires. This is how the prophecy is fulfilled in Christ. Malachi is saying to the Levitical priests who will not carry out their allotted inheritance that the Church of Messiah, made up of all the nations, will be faithful in theirs.