I think the author of the article pehaps chose ambiguous wording.
I'm guessing that the 1000 people are charged with committing a SAFE Act "crime" since the passage of the safe act, and are also charged with other offenses committed since the passage of the SAFE Act which, due to a part of the SAFE Act, will be charged as felonies rather than misdemeanors. I don't think the author is describing crimes committed before the SAFE Act.