In reading over this blog post by Tom Whitby and this post by someone about the negative end of this experience, it appears we may need to be more careful with the way backchannels are used. Obviously, the relative anonymous nature of Twitter allows cowards to be rude and unkind during presentations. Unfortunately, I don't think this will change but probably just needs to be tweaked.
Instead of allowing the Twitter stream to appear on the overhead, it should display only for the presenter (or a moderator) to see. Then the presenter can take what is relevant and professional and work it into the presentation as needed. I have seen a similar situation pulled off pretty well in some of my online graduate level courses.
While it certainly is an added skill and complication, with practice, many presenters may turn it into a positive experience - one that allows virtual "hand raising" and input with hardly any interruption.