I was somewhat irritated when Microsoft was pulling stuff like this with IE. But on the other hand, if they ever do make PNaCl, I will gladly disregard every other browser and target all my personal projects specifically for Chrome. The unfortunate thing is that I haven't seen any news or heard of any progress being made on PNaCl in a long time.
Indeed - having different compiled versions of your code go over the wire to the client simply because they're on a different architecture seems so... backward.