Zak, when admins are on, I try to balance out teams. Moving pros over to a team won't necessarily make the team better. Most of the time, the problem lies with the team as a whole and a general unwillingness to commit to performing objectives (terrorists) or defending properly (counter-terrorists). Even the shuffle command isn't perfect and we have to spam it several times to make sure it is relatively random and not too crazy.
As Ice said, auto-balancers are not perfect. In fact, they are meant to ensure that the teams have even numbers, not necessarily skill (although it does occasionally move the top one or two players over; see above for problem with that). In the end, it comes down to team unity. A terrorist team that rushes together and works together will almost undoubtedly win on Dust2, unless the entirety of the counter-terrorist team consists of players like DragOn, SFG, Ghonzo, etc., ok also d00b. Then you are in an actual stacked situation. However, in reality, that is rarely the case. In fact, I have been on teams where the individual players are really good, but due to crappy teamwork and lack of communication (or confusion in communication), the team loses and loses quickly.
Best thing you can do if you see a stacked team is to get other players to switch. Generally, good players will automatically do it themselves (aka, "Someone come to T," go spec, good player switches). Now that isn't always the case, but in the absence of an admin online or available, that is a good rule of thumb.