I have approximately 25 1 star wolves working security...it's essentially a wood/eye farm.

I believe, and from experience this has held true, that if you are nowhere near your base everything around it is "frozen" including any mobs that might have been attacking... like that annoying grey dwarf chucking pebbles :) If you left him there he will probably be there when you go back but he shouldn't have managed to raze your fortress :)

Yeah its true, nothing happens when you are not around. If you have a base far away in the woods it will be frozen in time until you return. This applies to mobs only though. If you have crops there they will continue to grow, torches and fires will continue to burn down, and smelters and kilns, and fermentors will continue to operate. (As long as you are in-game)

Build defences, so they cannot just walk in? A decent ditch is easy, fast and effective. Or if you have the tech, raise a wall from the earth.