You're putting way too much into Lincoln being blown up the next inning, chances are they would use somebody else. In a bases loaded scenario you really want to start looking at who is likely to be hit. You do raise the possibility that putting in new pitchers to bases loaded rarely works out, in that situation it may be true that its best to go with Lincoln. However, the Jays have a few relievers capable of having clean innings at all points in the game, and so if Janssen, who is a much superior reliever is comfortable in that situation to perform to his abilities (especially better than Lincoln, who obviously was not fit to handle it). They would also have the possibility of a second inning of Janssen, if they do score a run.