I can't argue with what you say, Harry, but you might also consider that not all coaches at the youth football level, always, have best intentions in mind. The requirements that all players play a certain number of downs is not intended to allow coaches to get their secondary players into the game, when it's long been decided.
Unfortunately, there are times when the officials are the only clear thinking adults present and rational, mature judgment needs to be applied. When such a situation arises, it has absolutely nothing to do with, "it's for the kids" and is all about some adult with an axe to grind, an ego to polish or to cover up for not allowing his secondary players to play meaningful downs.
In most situations, Time outs are the exclusive decision of coaches and we no input in how or when they are used, nor should we want to get involved. However, when you are certain they are being used to abuse a situation, you have to decide whether you are going to abett the abuse. Of course you have to be willing to defend your actions, but when you're right, doing what's right usually has less consequence that allowing something that's obviously wrong to go forward. It boils down to you making a management decision, that may not appeal to everyone on circumstances they may be unique to the situation you are dealing with.