According to the rulebook, the entire unit is marked activated upon the expenditure of all of the F.O.'s Actions; therefore, if the activated unit is not comprised entirely of models with indirect fire capability, the models without indirect fire are assumed to be "standing by" while the Speculative fire is performed. If the models have Ambush, two Actions may be placed on Wait. Otherwise, the only Action allowed by the models without indirect fire is to place an Action on Wait.
In other words, it is a decision that must be made by the player as to whether or not to commit the entire unit to the Fire Mission, or not. The F.O. cannot Give Orders to the unit; it may only Spot for Speculative Fire. The rest of the unit that is, subsequently, marked Activated is providing cover fire and awaiting the indirect fire-capable units to finish their "special action."