I'll begin here with a couple of presuppositions:
1) Pedro Alvarez is the starter at third, and Jose Tabata gets one of the corner outfield spots. That leaves two spots (first and a corner outfield spot) to discuss.
2) The Pirates have a variety of options to fill those two spots, and they shouldn't waste their time by playing Ryan Doumit there. (And they shouldn't have been playing Ryan Church there either.)
I think I and most of the folks who are regulars in the comments can probably agree on those two points. The problem is that the talents who are left to play first and the outfield are interesting but ultimately marginal. We can argue really passionately for Lastings Milledge one month, and then check back the next month and find he's hitting .264/.289/.333 after the break. Whoops! This doesn't mean that Milledge shouldn't be playing, and clearly he's a more interesting option than Doumit is, simply because he does have a chance of providing some future value. But he hasn't exactly seized a job, and most of the other players who might have claimed time are like him - it isn't that they're worthless, but they're marginal.
At this point, I think it makes a lot of sense to start Jeff Clement at first against a fair number of righties, with Garrett Jones in the outfield. Milledge can play against lefties and pick up occasional starts against righties. It would ultimately be good if Milledge could play every day against righties so that he could get better at hitting them, and certainly that would be smarter than playing Ryan Doumit in the outfield, but I'm no longer sure Milledge should get that luxury. Clement played well enough at Indianapolis to warrant another look at the major league level, and this might be one of the last clear shots he gets at one.
The problem is John Bowker. Bowker is very probably a marginal player, but he posted a .982 OPS at Fresno this year and currently has a 1.097 OPS at Indianapolis. Like Jones and Clement, Bowker is a lefty, so it's really tough to accommodate them all. Also, Clement and Bowker will be out of options next year, so there's a limited amount of time to learn anything about them. The only real way to find space on the roster for Bowker right now would be to send down Clement (or maybe to get rid of Delwyn Young, who's also out of options next year). So it makes sense to keep Bowker in Indianapolis until rosters expand in September, and see a bit more of Clement until then in order to clarify the battle between Clement and Bowker next year in Spring Training. In September, I wouldn't mind if there were situations where both Clement and Bowker started (at first and in the outfield, respectively) and Jones took a breather.
It probably isn't a life-or-death situation either way, but it is irritating to see Doumit and Young start in the outfield against righties when there are all these problems to resolve.