Sortrons are a terrible choice for people who aren't (at minimum) amateur computer programmers and have a deep understanding of the game mechanics of both Minecraft and its mods and love complexity for the sake of complexity. You really really really shouldn't be recommending them to newcomers even if you provide the code.
OK I accept that. It would be nice to have some other mechanism that doesn't get interrupted every time a piece of cobblestone - or any other high volume item such as dirt, gravel, sand, sandstone, red rock, cracked sand, or marble - appears in the first slot though. Sortron (or turtle's internal inventory) is the only way I can think of to do that, as you can force it to step through the slots rather than being reset every time the first slot gets an item. Also the OP isn't the only person reading this thread, and my reply might spur alternative buffering suggestions that I am unaware of.
Here's another idea. You could have a Filter set to pull full stacks of up to the 9 most common items - I list 8 above and can't think of any others - that is pulsed frequently; and a second Filter that is pulsed less frequently that pulls anything. That would provide a decent amount of stack consolidation, but would require two timers or one timer with a counter (e.g. pull full stacks on a 1 second timer, with a counter to pulse the "pull everything" filter on the 30th pulse). I find that a 27-second loop (1 second per slot, 27-slot enderchest) is easily adequate for a full-sped quarry, it usually builds up 3 and a half stacks of Cobblestone in that time, so a 30 second loop should be ok.
*Edit* Actually that isn't a great idea. The single pulse after 30 seconds would only retrieve one item. You'd need to pulse it rapidly to clear the backlog, and as soon as the first pulse happens, a piece of cobblestone will appear that will get pulled on the second pulse. Hm. Not good. This is precisely why I resorted to a Sortron.
Ooh I know! A frame machine above the quarry that pushes two Enderchests back and forth so one fills up while the other is being emptied... I'll get my coat.