When Chomsky says "rational" he means an act that furthers your self interest. The same way an economist would say "rational". "Irrational" in Chomsky speak means an act that harms the interests of the actor. Israel's barring of Chomsky only harmed Israel by shattering the idea that Israel tolerates free speech or academic freedom. Furthermore, Chomsky's ideas still leak in through the remaining press in Israel making the act of stopping even more futile. So no, Chomsky is correct, the government of Israel acted irrationally.
from the article: Otherwise Occupied / The irrational stage