We know that Clark Kent (Superman) is "allergic" to green Kryptonite. His blood "boils" around it and it may be fatal to him. He first came to Smallville in 1984 along with the debris from Krypton which contains green Kryptonite.
We see that the ship cannot block green Kryptonite in the season 2 finale "Exodus". Also the ship lacked the power to neutralize green Kryptonite as it did in "Visage" since during the entire space journey the ship had enough time and was in close enough proximity to green Kryptonite to neutralize all of it but this didn't happen as Kryptonite still landed in Smallville.
Therefore during the entire space journey, the baby Kal-El was in close proximity to green Kryptonite. **Shouldn't he have died due to the continual expos**ure?