If you are not willing to mute/ignore IMs while focusing they can be distracting and reduce productivity. However, if you aren't willing to mute/ignore I think the problem is not with instant messaging but your personal focus. Any form of communication can interrupt your workflow if you let it.
If everyone muted or ignored IMs whenever they were trying to focus on something, the whole purpose of instant messaging would fail; it would not be "instant" anymore, so we would all effectively go back to phone calls and e-mail.
Also very important: there is a huge design flaw in any piece of technology that, for it not to disrupt your entire life, you have to deliberately ignore it or find ways to not let it sabotage every action you try to take.
