Remember, S2 is basically complete. All the new network needs to do is pay for the rights, then put the show up. Continuing it is far more involved. While I would love to be proven wrong, I get the sense that two seasons is what we're getting.
I doubt a network would bother to pick up Prodigy if they weren't at least hoping it would do well enough to last more than one year. Yes, it's an easy investment to pick up a completed season, but the reason for making that investment is the hope of a longer-term payoff. Of course it's not guaranteed, but getting any show made or renewed is always an uphill battle. That's just par for the course.