I'm in pretty much the same position (one Google account for Analytics and Webmaster Tools and another for my personal Google Apps) and unfortunately the only solution I can suggest is to use a different browser for one of the tasks. I use Chrome for my regular browsing and then pop open IE when I need to access Analytics under my other account. It's not ideal but it's not overly cumbersome and I don't have to keep signing in and out so it is reasonable time-efficient.
I'm hoping that Google keeps up the improvements they started with their multi-account feature and extends this to all their Apps so everything just works a little better!