Think about this. The clutches in the differential will want to spin the opposite wheel, just like it would if it were jacked up and you spun one tire the other would spin the same way. Same thing on the ground and driving. There is no resistance in turning the other axle. It will also turn the drive shaft, again, very little resistance. You may feel a slight pull to one side but I doubt it. I run slugs for hubs in my Jeep due to grenading to many hubs. I also run a locker in the front. I have blown a u-joint in one axle and three wheeled all day and then drove home many miles with no issues at all, no pulling. They have come to the conclusion that there is so little gained by using locking hubs that few companies use them or the axle disconnects anymore.
I do agree that the manufacturers say not to put a LS in with a disconnect. That is more of a CYA thing than anything plus if you are putting a LS in the front you should already know to disable the disconnect. I am not disagreeing with the reasons, just the end result.