There was only one security problem in the whole CAN and that problem happened because Togo's staff didn't follow the rules. It's a pity what happened, but if they had followed the rules and only travelled by plane to Cabinda, none of this would happen.
Angola has severe security problems, but they cannot be blamed for this, they did an amazing job providing security to everyone involved in the CAN. Let's hope South Africa and Brazil are able to do such a nice job.
About Togo's suspension, I'm also against it, but these are FIFA laws, they don't accept any kind of interference from "outsiders". Some years ago a President of a club in Portugal, tried to stay in the first division appealing to regular courts and Portuguese Football Federation was warned that if any of their decisions were changed by a regular court order, Portugal would be out of Euro 2008 and the Portuguese teams wouldn't be able to play in that year's European Compe ions.