He was asked due to his actions he took after he was told to stop. If he had just stopped talking after being told his time was up he would not have been asked to leave.
The 1st amendment has long been understood to protect the content of your speech, not the time, place, or manner of your speech. It guarantees the communicative act, the viewpoint or message conveyed; it does not give you an unlimited right to convey it however you want. The government has been consistently allowed by the Supreme Court to establish noise ordinances preventing people from yelling into a bullhorn at night or laws against marching a protest down a busy city street without first obtaining a parade permit. As long as there is no viewpoint discrimination in how those laws are enforced, it is perfectly legal to restrict public comment periods to 3 minutes.
I don't get your point. Going over by 5 seconds didn't get him in trouble. The court can tolerate such minor mistakes as long as people are willing to behave themselves.