As my translator "Al Gharqad" notes:
"Allahuma alayka bil-yahud iz-zalimin il-jairin, Allahuma alayka bil-yahud il-mustakbirin il-mutajabbirin"
This means:
Allah, "alayka bi" the tyrannical and despotic Jews, Allah, "alayka bi" the arrogant and tyrant Jews
"Alayka bi" is a curse, which has no exact English translation. It is a prayer to Allah to do something with the subject of the curse. This "something" has been translated in many different ways:
1. "Take" (as in "kill"):
http://www.ctc.usma.edu/posts/imagery/0020
(second line from top)
2. "Destroy":
http://www.kalamullah.com/qunoot.html
(sixth Arabic paragraph from bottom)
3. "Deal with":
Egyptian President Morsi Joins Preacher in Prayer for Dispersal of the Jews
http://www.memritv.org/clip/en/3614.htm
(0:26)
Either way, he isn't calling for Allah to punish Zionists or Israelis - but Jews.
Qaradawi is perhaps the most popular preacher in the Sunni Muslim world and has famously encouraged suicide bombings.