If you have 50 PCs then automatic updates are best managed using something like Windows Server Update Services (WSUS) or Shavlik. WSUS is a free download from Microsoft and runs on your server, it acts as an update proxy (which will save you a lot of bandwidth), a management console that allows you to control which updates are deployed and a reporting engine that helps you determine which PCs are non-compliant.
I have never experienced an auto-update that required the user to go throught the WGA process. Add-on tools (like Windows Defender for XP) - yes, updates, no. Even if that is the case, WSUS enables you to pre-accept any EULAs on behalf of your users, so there should never be any interaction required by the users to install updates.
The effect of not going through the WGA process is that you don't get to install the product it is protecting.