I was actually with Ellen Johnson just hours after she recorded a segment with Glenn Beck on the above issue.  We watched it together, and I thought she was great a Glenn Beck was as obnoxious as usual.  The crosses were put on public property and I thought Ellen and American Atheists were in the right for getting behind the project.

To answer the question though, yes atheists can take it too far.  The line I use as a determination if it's too far or not, is the law.  If it violates the law, it's too far.  We must utilize our free speech rights if we expect to make progress, and the major atheist orgs must continue to fight battles in courts as well.  While these battles aren't necessarily going to win over Christians in public opinion polls, that shouldn't be our concern.  Our concern should be to fight for whats right at all times, even if it devastates the delicate sensibilities of people with imaginary friends who live in a magical fantasy world in which they and their religious leaders can do no wrong.  It's our job to teach them what's wrong and why.