Making that type of move in a regular-season game would constitute jerking around the starter. That would make little sense in the absence of a performance-based reason.
In this case, Harbaugh wants to see how Kaepernick and other select backups perform against another team's starting unit. That is exactly what a lot of us would like to see for players at various positions throughout the division.
Harbaugh thinks the experience could better prepare those backups for regular-season action if called upon down the line. At quarterback, Alex Smith will start and play perhaps two series. Kaepernick could then come into the game for a stretch before yielding to Smith. Coaches always reserve the right to adjust their approach should circumstances dictate, but I see no real downside for the 49ers.
Smith appears clearly established as the No. 1 quarterback at this point. Giving some first-team reps to Kaepernick should not significantly undercut Smith's short-term job security. Harbaugh, as a longtime NFL quarterback, understands the dynamics of the position.
This seems like a logical move and an example of a coach willing to defy convention when it makes sense to him. And if Kaepernick looks great, we'll have lots to talk about on the blog. I'm all for that, too.