I think that you don't have to worry about the first scenario all that much, other than the fact that it makes playing the infield in early in the game a non-option. Early in the game they aren't generally in, that would be a late game substitution situation on key runs, necessitating bagwell being yanked for a defensive replacement. 7th inning on I think you will just have to do that and replace Bags. Obviously when you have the infield in early you open yourself up to a big inning, so although you will give up one run more often then not, maybe you avoid the 2, 3 and 4 run innings by having the infield back, losing only a little bit in run prevention.
2 guys scoring in the scenario I thought you were talking about would be deadly- ie if that ends up developing you are giving away way too many runs, and you can't defensively substitute in the 4th inning for something like that, making bagwell a huge liability as oppoesed to a minor one. I would HOPE he could prevent scenario 2 from happening with a shot put, or getting the ball to the pitcher or 2b backing him up quickly, like when he used to flip to hidalgo occasionally. If he can't compensate for this though, he is less than worthless imo.