The other explanation given in the article was that playing the IF in might allow a play at the plate to preserve the lead. Unfortunately we got neither a play at the plate or a DP.
The bigger picture is that there were many reasons we lost the Philly series. You have cited questionable decisions by the manager, and there were some. I have cited other reasons. Roster mismanagement is debatable but the complete lack of offense (besides Yepez) is not debatable. We stunk on offense.
The truth is that all of the above led to the defeat. Blaming the series loss on just the manager seems like having an axe to grind instead of being a bit more objective, and more importantly, it lets everyone else off the hook.