Yes, there is only one kind of conversion in Israel....Orthodox. It doesn't say that the conversion is taking place in Israel. They are there now, for the filming...but there is no report as to whether it will be a Beit Din conversion. Natalie has never been an observant Jew....so, can't imagine any self-respecting rabbi wouldn't have some concerns.
from the article: Mazal Tov! Natalie Portman's husband converting to Judaism