It all depends on the situation. Of course, it would be nice to retire the side on three pitches, but what if you come into the game in relief in the middle of the inning and you have a couple of runners on base? Then you have no choice, especially with none or one out. You have to go for the strikeout. Here's a scenario: the starting pitcher is taken out of the game in the seventh inning, and you come in to relieve. The bases are loaded, and there's nobody out, and you're going to face a pinch-hitter you've never seen before. All right, what now?
You have to keep the guy on third from scoring.
So there is no clear-cut one-or-the-other answer to this particular question. You have to think about the situation and go to what you know about strategic pitching. I can give you an example, not only from my own experience but also from what I have seen in the major leagues any number of times. Bases loaded, nobody out, and you're facing an unfamiliar hitter. I saw many a pitcher do just this: he struck out the first two hitters he faced and then he got the next one to hit a weak grounder to first. End of inning, side retired. (Think Mariano Rivera.) Another pitcher would just strike out the side, which is not a bad way to get out of a jam like this. (Again, think Mariano Rivera.) However you do it, the essential thing is to keep the runner on third where he is and don't let him score. Having been a strategic pitcher, I think in those terms all the time. 8)