Hey Rei, I've been in the top 3 guilds for GT for a while now and know your pain. I generally place in the top 10 and used to have a hell of a time with customer service trying to get gems. So here's what has worked for me.
WIth 1 or 2 minutes left in GT, go to leagues, then click on Guild Tournament. Wait for the timer to go from 1 minutes then it will reset. At that point a screen will pop up showing the top 3 teams, hit continue, the next screen will award you the gems. I have been using this method for the last few months without fail. Yes, it does require you to stop raiding before the end of GT, but it's either that, or dealing with a dead end with customer service. This is only reliable way I have been able to get the gem reward for participation in GT.