"in on" is not really a preposition at all, it is a phrase that means "involved in" , "had inside information about" , or "knows about"
Example 1: If someone tells you a secret, then you are "in on" the secret.
Example 2: If you know the news, then you are "in on" the news.
You can rewrite the sentence as:
"If Snape was involved in protecting the Stone, it must have been..."
"If Snape had inside information about protecting the Stone, it must have been..."