The commander wanted rid of Nick a few episodes back. The death of his commander in the bombing gives CW the leeway to now remove Nick from his staff.
He doesn't have a bond to the baby so he's not so fussed what happens to him/her.
Besides which, I think he's quite possessive about June - her losing the baby means he could wangle it to keep her in the household.
So I'd say he did orchestrate their discovery - after all, the resident soldiers were very specific about "just ten minutes" but the commander had stated "back in three hours" to Nick/June. If he intended June & Nick to escape, he'd have been clearer with his instructions, removing June before Agnes, for example.
My theory anyway.
That said I'm usually wrong 