On the surface, the logical and "macho" answer is to go for the lead runner, but I would argue that it's not always the best strategy in fastpitch where the bases are shorter and double plays are less frequent ... and my guess is that it gets teams in more trouble than it gets them out of. Let me explain my point.
While people can say all they want to about pitchers' fielding, their main focus is always going to be on getting the hitter out. If they are thinking a lot about whether the runner on first is really fast, or is going on the play, or what am I going to do if the ball is hit back at me, they are not as focused on the hitter. Sorry but the pitcher and catcher have different priorities than the rest of the fielders who should definitely be thinking about these things.
Secondly, as JoeA says, pitchers and infields don't often get to practice these kinds of plays very much. Additionally, I think a lot of pitchers are so used to throwing underhanded, that they have difficulty making sharp overhand throws. And a play like this needs a sharp overhand throw.
Finally, I also think its depends a little bit more on the game situation. If that's the winning run out there, then the pitcher knows that and is going to try to make that play almost every time. But if they're up 5 runs in the 5th, why take the chance of giving the other team a big inning? I also feel a little differently about it if there's one out vs. none. If I can get the 2nd out of the inning at 1B easily, and am in the bottom part of the other team's lineup, then I might rather have an out than take a chance of putting 2 baserunners on.
Call it what you want ... I am just saying if you always do the "macho" thing in coaching, then be prepared to lose a few games that you might otherwise win.