Seattle only had 1 time out left. If they run on second down and goal at the 1 and don't get it, they have to burn their final timeout. Then they have to pass on third and/or fourth down or the clock runs out. So you basically only get 1 chance to run it in with Lynch (Yes, you could try to run on third down again but that's risky as if you don't get it, you won't get to even do 4th down from the 1 as the clock would run out)
But if you pass on 2nd down and don't get it, then you get TWO CHANCES with Lynch running the ball in from the 1. Incomplete on 2nd down. Run LyncH on third. If he doesn't score, call timeout and run him again on 4th.
So by passing there, you are setting yourself up for two possibly Lynch runs (and 3 total plays from the 1) versus most likely just having the 1 Lynch chance (and 2 total plays from the 1) if you run it on 2nd down.
PS. That being said, I think it's easier to stop a run off of an incompletion. Line gets a chance to regroup, lineup etc. The 1 thing you can't have happen is an INT. I very much didn't like how Lynch wasn't in the backfield at all. I'd at least have done play action. The WR would be wide open.