The phrase "Don't Be Evil" seems like a kitschy nod to Google's earlier days when they were just a couple of programmers in a garage. However, that was decades ago and Google has grown into a more matured entity. This statement comes from a time before Google had to meet with Government agencies on a (probably) daily basis or start policing YouTube for terrorist beheading videos and pornography. They are actively trying to do good - but they're no different than IT - you only complain about when things go wrong, never when they go right. Google does plenty of good, they don't need a snide comment about how everyone else doesn't to do that.
To remove this artifact of the past isn't to say "it's time to start being evil!". It's a child putting away their toys as they move to more mature times.
EDIT: As someone mentions, the line is still there. Leaving my post up as it still stands if they took it out tomorrow.