In this Luke passage, however, the soldiers ask John what they must do to repent and John tells them three things (NIV)- don't extort, don't accuse falsely, and be content with pay. What seems to be missing from John the Baptist's exhortation is that he doesn't tell the soldiers that they must leave the army. This seems to imply that being in the army - which would certainly mean doing bodily harm for some - was legitimate. So what do the pacifists have to say?
1) This is one of those passages where the translation makes a big difference. If you read the text from the KJV, John tells the men to - do no violence, don't accuse falsely, and be content with your wages. In fact, the rendering of this word as "extortion of money" is a very narrow reading, as most of the definitions for the Greek word used here involve physical violence.
Now if John is telling soldiers to do no violence, what might that mean for their career? It may mean they have to leave their profession (more on that here).
2. Even if we take the more generous interpretation for anti-pacifists, John the Baptist failing to tell soldiers to leave the army wouldn't be all that surprising. John was the last prophet of the OT. There were a number of times he didn't really understand Christ's way or what he was doing, and at one point he even sent messengers to ask Jesus if he really was the Messiah. Jesus was extremely revolutionary, and the extent of his Kingdom was not realized by any of his closest disciples until after the resurrection. John's failure to directly exhort soldiers to leave warfare wouldn't mean that much to me.
3. This argument is at best an argument from silence. Even if we take out alternate interpretations of the word "violence" and we assume that John knew exactly what Christ's kingdom was and how he would bring it, this passage would still say nothing of itself about violence. It may be an interesting piece of evidence to bolster an already strong case, but I don't think anti-pacifists have much of a foundation for this verse to be very helpful to them.