So I'm wanting to do an indoor refuse and I'm just wondering - if I have a single tile channeled from the surface down to where my refuse is, will this allow the whole room to be light above ground or does it have to be every tile of the room? If the resulting tiles are still dark subterranean, will the chimney prevent miasma anyway?
Channel the whole room. If you are worried that a siege may come during the work (most probably during the covering phase, which takes more time than channelling) then just do not connect the future butchery to the rest of the fortress yet. Do it after it is secured, i.e. covered.
Will bars or grates be sufficient protection or will building destroyers still path down?
Building destroyers when enter the map do path to the closest building to them, not looking at such trifle obstacles like earth. But they re-focus as soon as they see other more significant targets (for example dwarves), so you can protect the area with important buildings easily, by burying them deep in the fortress, or surrounding with walls and other structures. But doesn't matter - the best thing to do after channelling is to cover it with floors of any material - building destroyers won't touch it, and the covered tiles will still be preventing miasma formation.
Also, buildings means not only workshops and grates but also doors. You can just have a series of doors installed to stall the destroyers.