The phrase has its origins in the practice of "jumping" and robbing people in gay havens and brothels of the 19th century because no one would report the crimes.
"Molly" meant a gay or effeminate man. "Molly houses" were gay (male or female) and cross dresser's brothels or hang outs. The "hop" or "wopped" (probably now used more in the east coast, and the UK) was first used in London and New York and slightly altered in pronunciation and meaning as it filtered over time and space. Now anyone can get molly-hopped. Unsurprisingly though it still is most often used when a woman (especially a woman who is "street" herself), or effeminate man (or just a man deemed to be a chump) is assaulted in this way.
Look at your eye! Raneekwa molly-hopped your a$$ huh. When she came up behind you I knew it was on.