Other than fatigue, I don't see a reason to pull a pitcher since the Sim does not program for Good Days and Bad Days. Assuming your settings are as you want them, it's safe to say the guy on the mound is the best available. The fact he gave up two runs has no impact on his performance versus the next batter - which should have a better average outcome for you than if he were pulled, since your current pitcher is the best available.
Of course, my teams have been sucking lately so take my opinion with a grain of solt - or an entire salt lick, for that matter...