Challenging the legitimacy of a country isn't the same thing as calling for its annihilation.
Many people challenged the legitimacy of apartheid South Africa. What they wanted was a total transformation, not annihilation, nor for the expulsion of the white population.

It is also perfectly fair to see countries such as the USA and Australia as having been built on a total illegitimate basis of annexation, theft and genocide. But that isn't the same as saying these countries should cease to exist.

It is perfectly possible to challenge the legitimacy of the status quo as regard Israel, seen as a situation in which a state defined as confessionally Jewish, on the basis of past ethnic cleansing, occupies and controls the West Bank, and imposes a territorial blockade imprisoning the Gaza strip, The inhabitants of these territories are in effect living in Greater Israel, but with no effective political rights.

That analysis can be challenged, and is challenged - but I cannot see how it can rightly be identified with antisemitism.