Among many problems: when applications exploit Twitter metadata to send unwanted unsolicited messages, that makes users far less willing to authenticate other apps to Twitter. I'm already paranoid about doing that (and Facebook authentication), because who knows how the app will choose to embarrass me?
The bigger issue is that if there was no punishment, everyone else would now be trying to use the same tactics Meerkat did in order to spam people and obtain growth, which does result in a negative Twitter experience in the long run.
Startups will probably still try to do it anyways, though.
He knew it was coming, he knew it was wrong. Why would he need more warning than two hours? Why even a warning?