Ra1th,
I agree with much of what you say. From an unbiased, rational point of view, Angel probably did what he had to do by leaving his post to investigate the alarm. The problem is, once everyone finds out what happens and shit starts to hit the fan, people aren't going to be rational or unbiased. There is going to be panic and chaos. And Angel is going to end up with the blame.
Someone, most likely Michael among others will probably stick up for him eventually, but people are still going to blame Angel for what happened. And Angel will probably end up blaming himself to some degree also. It might not be fair but its going to happen. People are going to look for a scapegoat to blame for this, and until the culprit is found Angel (assuming he isn't the culprit himself) is the easiest scapegoat.
And this is what puts another nail in the "will Angel ever become leader of the Tower" question. This sort of thing just keeps happening to him. He gets blamed for things that aren't necessarily his fault. He makes rational decisions that turn out to bite him on the ass (wanting to leave Burt behind, wanting to not let Lizzie and her boyfriend in because it was too dangerous, etc...) These are the sorts of things that on paper seems rational but make people angry. And now people are going to see him as failing to save Pippin and Hope (if Hope was killed). People just aren't going to want him as leader if that's the way they see him. Is that fair? Absolutely not! But whoever said life was fair?