Haha, I remember those arguments. I always liked that he made that spell choice from a character perspective anyway, but it didn't really register with me the first time that he was actually using it now.
I noticed that too, and I actually think they both made the right choices. Roy knew that he had to try to stop Xykon to have any chance of saving the Azurites (among others) who would otherwise die at Xykon's hand. Taking Xykon up on his offer would have ensured their deaths, so he had to try to fight.
When Elan takes up Tarquin's offer on the other hand, the situation is slightly different. Once Elan discovers that he can't defeat Tarquin, the best chance he had of saving the people that Tarquin threatens was indeed to retreat and regroup, and unlike at Azure City, there were no immediate casualties to be prevented by Elan forcing a fight that he couldn't win. The fact that his first thought after running away is to find Haley to get help in finding a way to defeat his father shows that his heart was in the right place.
So, I'd say Roy and Elan were both doing what they had to in order to have the best chance of protecting people from evil--in Roy's case, backing down had no chance of protecting anyone, but in Elan's case, it's continuing to fight that would have sabotaged future efforts to save people.