What religion were your Cherry ancestors? According to immigration records there are many Kirschner arriving in the US at various times. Some of these are Jewish according to their given names. Many of the Kirschner are from Germany, Austria, etc. Kirschner is the closest to Cherry in German, as a surname. There are no records of any people who had Slovenian surnames that mean Cherry in English.
There is a Michael Kirschner who arrived in Sept. 1884, and was born in 1872. However, he can be found in New York in the 1900 census with his wife Adele and family.
I would suggest finding the marriage record for your Michael and Mary, or possibly the birth records of the children. It is very unlikely that his surname was changed during immigration. He probably changed it after he settled in the US. Rather than trying to look for possible names which translate into Cherry, I would suggest trying to go with what you have. ie. the paper-trail on Michael and Mary, until you exhaust all avenues there. There may be a clue in the marriage or birth records, or in his naturalization application. If you know that he lived in Allegheny PA during the entire time, try looking at local newspapers if there is any official notice of a name change.