I'm going to slice and dice here. Most of the stuff you said I agree with, and everything was perfectly understandable from a coaching and player perspective.
1) Both safeties are smart. And we want them communicating with each other, but we don't want them giving out conflicting calls.
If they are both smart and you want them communicating, let them both give out the calls, but tell them disagreements are not acceptable. They'll figure out how to work together (good) or they'll figure out that one of them is better than the other and one will defer. (better than what you may have right now) Either way you'll have them both thinking and if one goes down the other will be in a better position to step up.
The situation I'm thinking of here is freshman year of high school, where it was the strong safety's "job" to set strength but the free safety's job to lead the huddle and then make coverage adjustments. Well the free safety had trouble with formation recognition so basically the strong safety often had to "suggest" the formation name and sometimes even feed him his lines as it were. rather than dump everything on the strong safety the coach gave them both wristbands and told them to work out formation calls together, which worked out swimmingly. At first, they would confer before the snap in a conversational tone, then one, the other or both would make the announcement. By midseason they no longer needed to confer, they just both made announcements. At the very least psychologically it was advantageous to distribute the responsibility like that.
I understand that at the age you coach, that could easily devolve into squabbling.
3) The motion happened so late that if we did shift, we would have had both safeties in transition at the snap. In C3 the SS walks up and has force, he would have had a mere moment to drop back 8 yards to get in position and make sure the OLB on the opposite side of the field was now aware of the change and that he now had flat vs curl to hook. That is a lot of moving parts at the snap of the ball and nothing good will come of that situation. Hence its best to be wrong together then have one player out of place.
Okay, this is definitely an extenuating circumstance, and I know what you say here isn't exactly how you coach the players, I don't have a good grasp on that but: Don't call them "wrong together" then. Give your secondary players a rule or guideline about coverage changes at the snap. I've been given rules both of the "no changes on late motion" variety and "make this automatic change on late motion" variety. Late motion happens. Give the players clear ideas of the right and wrong way to deal with it. If you tell your secondary, or the safeties, or just the one safety, "do not change coverage after this point" then you've given them the ability to make the "right" decision together instead of telling them "we can live with you all being wrong together" and "you were both technically correct at the times you made the call."
The other thing I would say is to not be afraid of having secondary players in transition at the snap. QBs don't like that any more than you do. Probably less. If you don't want that OLB moving around that's one thing but safeties, who cares what they're doing as long as they're making the QB nervous and they can get where they need faster than a receiver or a running back.
You are right, teach them to do their job, but every defense has someone responsible for the calls at LB and in the secondary. Because not every player can see the entire formation. A CB split out is not going to be able to see a late motion on the other side of the field and adjust. That is not where his attention should be with a snap imminent.
That's true, and that's why communication - "twins right!" "two back" "motion motion motion" "watch crack" - is important. Always like arraignments where the information was passed instead of the coverage call. Gave me a better idea of what was going to happen. Like if I have twins to my side, then get a motion my side call, I both know the coverage adjustment if any and also that I'm likely looking at a levels-route situation.
You are right, your players are young and very inexperienced, and it is still early in the season (most likely). But you seem to have at least two players capable of making coverage calls. When I have played football, when coaches have allowed responsibility to be distributed as players are able to handle it, there have always been tangible rewards in the level of play.