At that time of night, the immigration line in BOG is always like that. The airport is simply too small for the amount of passengers. They did recently expand the number of passport control booths, so even though the line is long, it moves very fast. It usually takes no more than 30 minutes to get through the regular queue.

Still, I'm glad that you finally found the Avianca agent to take you to the front of the line. That indeed is standard practice, without which no-one would make their domestic connecting flights.