"Stick it to the man!" Mathematical discoveries that resulted in persecution.

Here is a rather comical one.

Henry Oldenburg founded the Royal Society (in London) in 1662.

If an effort to publish high quality papers, he had to correspond with many foreigners across Europe. The high volume of foreign correspondence came to the attention of authorities. He was arrested as a spy and held in the Tower of London for several months.

For his mathematical achievements, Cantor was ostracized by the mathematical community. Instead of being given the professorship he deserved, he ended up teaching in what was effectively a community college. He slowly went insane after that.

Describing the mathematics of Cantor, Poincare is famously quoted as saying that "later generations will regard Mengenlehre (set theory) as a disease from which one has recovered".

Source: http://topdocumentaryfilms.com/dangerous-knowledge/

Israel Gelfand discovered the tridiagonal matrix algorithm (or rather established its stability and applied to numerical solution of PDEs) in the early 50s . In view of the main applications of numerical analysis at that time the method - essentially an elementary linear algebra - was classified by the Soviet government services and Gelfand was forbidden to leave the country. Being a major mathematician of the epoch, he was therefore unable to participate in any conference abroad until (?) the late 70s.

There was an acerbic dispute between David Hilbert and L.E.J. Brouwer in the beginning of the 20th century. Basically, the former found the latter's insistence on constructivist methods ever more annoying. The animosity had eventually led to Brouwer's isolation within the scientific community. Brouwer survived his exile by almost forty years and died at an old age—in a car accident.