Now that's the thing that IC2 has been missing since its beginning.
Judging from the screenshots, I believe the quarry strips patches of the ground from the top to the bottom, meaning it has to load several chunks at once, right? Have you, perchance, considered implementing the extrautilities quarry mining algorithm (you dig the column all the way down first, then start another column)? This way you would always have to load only one chunk regardless of the mining area size (which you could then increase )?
Also, how about replacing the mined area with a block of your choice (dunno, cobble, gravel, dirt, stone)? Or are you that set on leaving huge holes in the ground?
Do forgive me for suggesting your quarry to become a copy of the extrautils Ender Quarry, but your mod has a huge advantage over extrautils - it doesn't require installing a set of needless items to get only one machine that does what I want it to do.