Wrathmonk,
I discussed this with a colleague today. The solution, certainly in the RAF was quite simple and indeed my previous experience actually points the same way.
Yes, the sqn cdr leads his sqn through training in to war and leads in battle. To provide the much needed operational control when the sqn cdr is in rest was quite simple. The sqn was effectively commanded by a gp capt. Indeed the EAWs are also, I believe, commanded by gp capts.
So yes, a sqn cdr should lead his men.