In 1:49 Hashem tell Moshe not to count to tribe of Levi. Rashi explains that Hashem knew that all those counted here would eventually receive a punishment of death in the desert. So why not Levi? because Levi is special. Levi did not sin by the Golden Calf. Levi stepped up to the plate and batted on God's side.
Why is that a reason - did we not learn by the children of Aharon the concept of "בקרובי אקדש" - that Hashem's name gets honored more when people see those who are close to Him being punished?
I am not saying Levi deserved death, but why do they get this special protection just because they were more purely dedicated to God, when we see others do not get that "protexia"?