I wouldn't say he becomes less effective...he can make throws Alex can't and, quite frankly, wouldn't even dream about making because of his history. Sometimes, you just gotta throw it up and let the receiver make a play. I think Kaep is much more likely to do that than Alex is.
For example, look at this throw to Manningham
That's a throw Alex can't make and would never make; From the right hash throwing back across the field to the left sideline with pressure in his face while Manningham is covered? Alex would've taken the sack. Kaep lets it fly.
I'm not saying in the long run that Kaep gives us the better chance to win or that we need him as the full time starter now. I'm just saying that if we have to go into this game with Kaep as the quarterback, I'm confident that he'll do just fine and we can win this game.