Note: I haven't played SC2 so this information might not be 100% accurate, but I have played D3 and WoW and I think they use pretty much the same launcher, but for a different game. This answer is based on those two launchers, and I'm assuming here the SC2 launcher works in the same way.
When you close the launcher at any time, the next time it will resume where it left off. When the updating process seems to 'hang' just close it and restart. Disabling your firewall should not matter, unless your configuration is non-standard (you or your network administrator tweaked the settings). Your virus scanner, however, can greatly hold back anything, so disabling it might help a lot.
Another thing is your internet connection itself, if your connection is slow, the updating process will be slow. If you are using a wireless connection, try putting a cable in and see if that helps. As I'm typing this I realize you are not updating, but reconfiguring, which has nothing to do with your internet speed.
A third option would be your hard drive. If your hard drive is slow, writing to it will be slow and updating a game might take long (not 30 minutes for 0.1% though). For optimal performance, install games that have to update a lot to your fastest possible hard drive. If you have an solid state drive (SSD), install the game on that one. You can tell how fast a hard drive is by looking at how much rpm it has (rounds per minute), the higher this number, the faster the drive. SSD speeds are expressed in MB/s write speed and MB/s read speed and they are generally always faster than hard drives.
Also, having as few applications running as possible will speed up everything that IS running on your computer. A few common things that soak up processor speed are browsers, skype, games and music/video players. Search for 'msconfig.exe' in the windows search bar and go to the 'startup' tab. Here you will see all things that are going to start when you turn on your computer, all of these programs slow down the startup process and keep using processor power, even when you don't use them. You can disable anything here, unless you really want to keep it as a startup item (some people like it when for example skype starts when they turn their computer on).
One last thing, which will probably not influence the SC2 updating/reconfiguring process, but does help speed up your computer, is to set the windows theme to something else then aero. To do this right click somewhere on your desktop -> personalize, then click any of the standard themes. Windows aero soaks up processor power and ram, and is there purely for cosmetics.