Dear OP

I sympathize with you as I experienced something similar even if in my case I was rebooked free of charge since the inbound was delayed. IME, however, the gate agents are not flexible at all. At T-45 the gate is closed and all passengers who have not arrived there are offloaded. If your inbound was ontime, or not delayed enough to be under the minimum connecting time, you are deemed responsible for the missed connection and most of the time you will have to pay to be rebooked. I assume this is what happened in your case. I do not believe you will have much luck in complaining with EK.

Just my 2 cents but based on my own experience.

Hope you can solve everything for the best.