Paul Kalchik, formerly of Resurrection Catholic Church, burned the flag last week along with a small group of parishioners. The flag had once hung inside the sanctuary and Kalchik called the burning an "exorcism."
Protesters called for his removal earlier this week, holding signs that said "hate is not holy."
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A letter signed by Cardinal Blase Cupich and dated Sept. 21, said, in part:
"For some weeks now, I have become increasingly concerned about a number of issues at Resurrection Parish. It has become clear to me that Fr. Kalchik must take time away from the parish to receive pastoral support so his needs can be assessed. ... I do not take this step lightly. Rather, I act out of concern for Fr Kalchik's welfare and that of the people of Resurrection Parish. I have a responsibility to be supportive of our priests when they have difficulties, but I also have a duty to ensure that those who serve our faithful are fully able to minister to them in the way the Church expects."
News of his removal, by the archdiocese was delivered at Saturday's afternoon Mass.
"I was sitting there and the priest who was giving mass got up to give the sermon and said in lieu of a sermon, I have a letter from Cardinal Cupich," said Rick Garcia, who is both a devout Catholic and an LGBTQ activist.
Garcia, who refrained from criticizing Kalchik, praised Cupich. "Our cardinal did two things. He stood with gay and lesbian people and he made sure that one of his priests gets the necessary help that he needs. My heart overflows for that."
Sunday morning, rainbow flags adorned the outside of the church and some parishioners were divided on the decision.
"I think it was very, very heavy handed that way that the Cardinal dealt with Father Kalchik. He hasn't been accused of doing anything wrong," said Paul Wierzbowski.
In response to the removal, Ald. Deb Mell (33rd Ward) said: "In situations like this, there is no other recourse. It's just better to get it done. We hope Father Paul gets the help he needs and we wish him well."
Msgr. James Kaczorowski, Pastor of Queen of Angels Parish and Dean, was appointed as administrator of Resurrection Parish, effective Friday, the letter said.
Cupich did not indicate whether the removal was permanent.