This sucks and I don't think it's fair to blame Farrell. Ortiz had to come out, it's logical to use a pitcher there. No problem
What this highlights is how collassally stupid it is to play baseball by NL rules in the year 2016. Having pitchers hit and run the bases is equivalent to a hockey team asking it's backup goalie to play center. Even NL teams usually use the DH in their minor league games, and that just proves how unimportant it is to develop pitchers as hitters.
The world is specialized. Deal with it.