In 2017 Morlino, arranged for a memo to be sent by his vicar general to all local priests, informing them that they may deny Catholic funerals to people who had entered into same-sex public civil unions or marriages "to avoid public scandal of the faithful." The memo advised clergy to consider whether the deceased or the living partner was a "promoter of the 'gay' lifestyle." To minimize scandal, the deceased's partner should have no public role in any ecclesiastical funeral rite or service.[7][8] A petition seeking to remove Morlino as bishop generated support from thousands of people.[9]

During the clerical sex abuse scandals in the summer of 2018, Morlino wrote a five-page letter in which he decried the abuse of minors, and described a "homosexual subculture" that facilitates homosexual sexual activities between priests and other adults.[10] Morlino wrote, "There has been a great deal of effort to keep separate acts which fall under the category of now-culturally-acceptable acts of homosexuality from the publically-deplorable acts of pedophilia. That is to say, until recently the problems of the Church have been painted purely as problems of pedophilia — this despite clear evidence to the contrary. It is time to be honest that the problems are both and they are more."[10] Morlino decried clerical abuse of minors, Cardinal Theodore McCarrick's sexual harassment and abuse of adult seminarians, and an alleged network of sexually active gay priests; interpreters of the letter disagreed on whether he was conflating these three matters. Some interpreted Molino as linking homosexuality with pedophilia, and countered by citing studies showing a lack of correlation between pedophilia and homosexuality. Others said that the vast majority of victims were male and that many were not prepubescent, therefore saying that the problem was more closely linked to homosexuality than paedophilia.[11][12] Morlino urged victims to report accusations to the police, and called for reparation as well as prayer and fasting to atone for the offenses.[12]