Based on actual data from 2002-09 the stolen base percentage of a runner decreases if at least one throw is made over to first by the pitcher:
No Throw Made 75% At Least One Throw Made 64%
In fact, it even makes a difference if he makes more than one throw:
One Throw Made 66% Two Throws Made 65% Three or More 64%
Both of these conclusions match what we found last time. If it's your pitcher making the throws, cheer him on. But if it's the opposing pitcher, it's your job as a fan to let him know that you don't appreciate all those throws!
So the more throws, the worse chance the baserunner has of stealing second.