Cromwell saved England from monarchs and helped move it away from the papacy. Unfortunately England fell and went back into the slavery of monarchist rule.
As for the Jesuits disliking him, yes, they saw he was recording the method of the Borgias who he once worked for. His book was listed on the index of forbidden books precisely because it carefully documented the behaviors extant in the Vatican and the city states.
Machiavelli was essentially warning the world of what despots do and how they behave. He wrote from a view in the middle of it where he carefully was able to survive. He was tortured by the Medici family. He fell in with poets and writers. He never held high office as a ruler, and perpetrated no atrocities. His book was a warning about the kind of people surrounding him in renaissance Italy. Some Vatican, some from noble families running the city states.
Is a shame to see people believe he thought his prince was his dream. It was his nightmare.
Yes, the Wheel of Fortuna was not very kind to him.