Time and period don't mix with ASL. .
They could, given a decent set of rules (which I suspect these aren't) and some imagination. John Hill would probably think so - the game system at its core doesn't model small arms ballistics, it models morale. A cursory reading of The Red Badge of Courage (fiction, you say? So was a lot of Enemy at the Gates, the inspiration for Squad Leader) suggests that the basics of Squad Leader (and later ASL) apply equally - leadership, morale, routing. One review of the original Squad Leader actually suggested the leadership model in SL/ASL is *more* suited to the American Civil War than to World War II.
A squad counter is an undefined number of men - sometimes 5 or 6 men, sometimes as many as 15, depending on nationality. During the game, individuals die, get wounded, panic, etc. in an abstract way. It would be relatively trivial to change the scale of the counters from squads to entire companies, given the tactics of the day. The IFT acts exactly the same regardless if it is matchlocks, flintlocks, muzzle loaders, or assault rifles - you will either drive the enemy from the field entirely with a volley, discomfit them, or have no effect. You might not have Point Blank Fire in ACW rules (no hand grenades) but then again given the very short effective range of aimed fire, perhaps you would.
Nothing on the face of it rules ACW combat out of a modified ASL rules set; the original SL was purposefully designed to be abstract and capture the very basics of infantry combat.