If I remember correctly, D&DH had an article in the past year that advocates shooting sub-dominant does and leaving the matriarchs.
All I can say for sure is that I've shot the lead doe once, back in 2004. She was a biggun too-- went 170 lbs live weight. After that, that doe group altered its patterns tremendously. This year is the first time I'm seeing intense sign around the stand where I took her.
On the other hand, I've got a stand about 500 yards away that sees us taking 2 deer a year like clockwork, but so far we've only taken bucks and small doe from it.
I don't mean to say that killing a matriarch will queer a stand quicker than other deer. What I am saying is that in this one case regular sightings of an established herd ceased after I shot the lead doe, and overall sign went down significantly. Scrapes that had been active for multiple seasons went unused. Rub lines ended. Visits to the salt lick went way down. Now, 4 seasons later, I'm picking up all sorts of sign again, and deer are using the same paths that were worn deeply up until 2004.
Once a hunter thinks he has the deer pegged, it never fails the deer will do something else. It's kinda hard to single out any one action resulting in a certain re-action. I do know what your getting at, and have seen similar results here, when harvesting doe's out of a group of deer in plain view of the shot. Something else you need to consider is that over time deer will change thier travel patterns instinctively, even within a small parcel. Some of that change could be due to evadeing predators among other reasons. However a few trails may have been used naturaly for ages, such as trails along natural water sheds, steep ravines,etc. I think as long as you have young doe's using trails, a few bucks will travel them during the rut sooner or later. No dought about the fact that if you havest the dominate doe in a area, the effect can reap havoc on the rest of the doe family. They might relocate the bedding area, or change feeding area's without the "mother" to guide them with her set way of doing things. Sometimes it will take quite a while for a replacement doe to move in on an deceased dominate doe's core area. In my area I have what is called a "doe sink", so replacement doesn't take as long as it would with a area that has a less quality habitat. This is why it's good to have a balanced age structure of female deer(and bucks), but when dealing with over population you have to start taking any doe presented, until you start to see results in your management efforts.