"Runner A is our most talented runner and runs maybe 20 mpw and competes primarily for the 3200 (10:22). Runner B works hard all year about 50-60mpw, not much talent but is just as good as A because he works hard for it, he runs 1600 (4:43). C & D dont really do much and aren't talented, but they still somewhat try if that makes sense."
I'm surprised this have never happened to you before. Your problem started way in advance of the race, probably at the point that you let your runners do whatever the hell they wanted to. You have a "talented" runner (if 10:22 qualifies as talented - in his own mind perhaps) that you let slack off. Can't imagine why you have two other runners (C & D) who don't do much and aren't talented - tends to go hand in hand - don't do much and get beat ... crazy, I know. If C & D see you consider A talented and allow him to do nothing (20 mpw is nothing), then why would they try hard to improve. You set the tone for having a lazy, uncommitted team. Sorry, just the way it is.
What you should have done is taken runner A and found a meet where the other 3200 meter runners would have beat him soundly. It would be nice if you could have found a sub 9:05 3200 m runner to lap him, but any race where he looks over when he hears the gun/bell go off and realizes he's 300 meters off the lead would work well. Then he might stop thinking he's a legend in his own mind and work to actually have a respectable 3200 meter time. In him getting beat handily in that same race, C & D might realize A is not that good and maybe they don't want to train as haphazardly as they currently do. Besides if C was so mad, why didn't he train harder? Again, if you don't put in the work, shut up and stop complaining.
As for runner B, I agree that race strategies and team/individual goals should have been discussed well before the meet. You could have rearranged your relay team order. Regardless, if B pulled that stunt, I think your only response would have been to pull him from his individual race and end his season right there. Why didn't runner B actually try to encourage his teammates to actually train and try to get better. I wasn't the best guy on my track team, but I trained hard, and was the one that got everyone out to practice daily and made sure we put in an honest effort. I wasn't even a captain, and the freshmen that made up half the team laughed at me all the time. But they came to practice when I organized it, they ran hard, and two of them ran 4:31 and 9:54 respectively (plus both under 16:35 in cross).
Coach, get some courage and take control of your team. Again, I can't imagine that you never ran into this problem in fourteen years. If not, you've probably just been lucky. Of course, after this whole circus was allowed to play out, I'm sure your younger runners who are returning next year learned valuable lessons, mostly likely that they can do whatever they want and blame everyone else, do what they want, and continue to think of themselves as better than they are.
Sorry to be harsh, but you can do better, for yourself and your runners. Take this opportunity and grow from it.