Well guys its a big point to think about that can Google penalize a site if we don't use Google tools properly.
I highly doubt Google penalizes site for using their tools. I would think it would be the other way around. Unless someone has something to hide of course.
I think if you play with analytic setting a lot it might happen. We use it a lot at work, and I mean all the time doing reports etc. and have been doing for over a year now and it has never made any difference - all it has done is allow us to see how our site is doing and now over 550,000 unique per month.Some person thinks that this is not possible,and some think that this is impossible.
I took survey on that and i found that some webmaster doubt that using tools will penalize the site, Some told that there might be other reasons for penalization or may be the competitors improved faster than you did over a short period of time and that made your rankings drop.
This might be the one possibility but ,as by using Google tools we are allowing Google to access over activities(over website)and if we do some Black hat SEO,Google easily recognize the bad activity,so it is possible that Google may penalize our site.
But that is just my opinion,and that is one side of using Google anyltics
Google analytic is a tool used to help find areas of your site on which you can improve. I agree that it would give Google as a company the ability to access more of your sites information, but if your using white hat SEO methods you should have nothing to worry about.