remember the chunin exam?
at the tower they said that heaven is brain and earth is body, so maybe it means that Kimimaru has a strong brain and will, but he's ill and lacks "earth", pyhsical fittness. while Sasuke's body is powerfull while his mind is weak and sick, so he needs a 'heaven seal'. it can also show that Orochimaru prefers a sick mind with a healthy body over a normal person with a weak body...

just my random 2 cents.