Yes. Yahoo and Microsoft both have newer tracking systems than Google Analytics. They are both superior in many regards. Look up "Indextools" and "Gatineaux".
Of course - those companies probaby have a similar vested interest in the data. But that's what you get with a fee product.
You will only be able to log in to your GA tracking system if you are logged in to a Google ID. Can you do this on a proxy server without google being able to see your computer? Possibly. But I am not entirely sure you will then have circumnavigated the potential issue. If you are using a proxy service and you are the only user on that service that is doing this, then does it matter to Google? You have associated the various websites by virtue of the way in which you have accessed the data. Indeed - there is a very real possibility that... algorithmically and without human intervention... your sites start to get associated with other sites not within your control, as part of the "group of sites that gets accessed from the proxy's IP". Not necessarily an improvement in your position!
So... yes... I personally think you are right to be paranoid. But then I am generally paranoid. No - I think you will need to do more than use a proxy to retain your anonymity.
It gets worse, really, when you look at the long term. As Google starts to control traffic patterns, it will use this knowledge to make the experience BETTER for users. If you don't participate and give it up to Google, you'll eventually lose the traffic anyway, I assume.
Nobody has to be trying to do anythin underhand in this scenario... but when you consider the fallout, I think that the result will be a private company controlling the virtual world instead of the people, or govenments or anything... you know... elected.