Well, a similar thing happened in era 74, where a team just stacked their entire army on a relic in the pacific and we had to fly out to take it with all 12 members - it could have resulted in how it did for you and cost us the era unfairly.
Tom ultimately decided to resolve the situation by stating that in future eras, relics would be taken back to land if the team that held them was dead/conquered etc or just trying to extend the era. The issue was then that he didn't do that this era, but changed his mind again and sent them to AA where it made essentially no difference. I don't think the relic speed thing helps either because it still results in annoying situations as happened just now.
The thing is, this only really happens on E3. But I do think that something should be done. The key needs to be making sure that everybody is informed about any unique rules - as they generally are in, say, E5. Because nobody plays every E3 and so people aren't gonna be aware of rules made say five eras previously.
Perhaps it could be sent out in the Admin's player message each era?