The French Team being Infected

I was a little confused when Ben was instruced to kill everyone in the French team because they were infected. So why was Alex not infected? Why did Ben let Rouseau live if he never wanted Alex to meet her? And as a side note to follow some of the religious parallels, Rouseau and Alex were a version of Moses. All the Hebrew were supposed to be killed, but baby Moses got to live and raised by Egyptian (hmmm-)family.

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