I made the recommended XML change in that thread, and I'm loving it. As long as you aren't in the habit of forcing end turns (shift-enter) all the time, you won't miss any opportunities to issue orders to units. The command bar will say "A Unit Needs Orders" if that is the case, and won't end turn until they all have been dealt with. Even then, it won't auto end turn if you have that option turned on.
I've found it's actually easier to deal with "Auto End Turn" after the change as well. Before, I found myself missing opportunities to do something like build on a new culturally acquired tile as soon as it was available because I couldn't wake up the worker in time (and was too lazy to move my hand to the escape key to turn AET off in the menu, heh). Likewise for say, not getting a barb that came into range because my warrior was fortified.
If you turn on AET, and turn off unit cycling, your turn is not automatically ended as long as you have a unit selected. It basically boils down to this - if you hit 'w' (wait) after you've given an order to your last unit on a given turn, it will deselect him. Now your turn will autoend - and as long as no units need orders next turn (say you have a worker building, a warrior fortified, and a caravel on auto-explore) no unit will be selected by the game. So, your turn will end, and end, and end, and end...until say the worker finishes his task. This is just like before - and you may fear you will miss an opportunity. However, all you have to do to break the cycle at any time is simply select a unit (like with the mouse). Say for instance, I select the worker while he's building. When the AI turns are finished, I will have the worker selected and be sitting on end turn. At this point I can command any other unit, or change what he's doing, etc... Note, I didn't have to hit escape, furiously spam 'wake' on any unit, or try to issue a "move to the hex I'm already standing on" order to break AET (all things I've done before, heh). I find it rather convenient because it's AET when you want it and Manual ET when you don't - and going between the two is one mouse click.