Actually you can use the console to remove them,
Look at this thread here, it's the clearwife command.
http://forum.1cpublishing.eu/showthread.php?t=4934
Note you keep your wife it just removes the children.
I used this quite successfully in my playthrough. I also tried having more children, but I seemed to get the same crappy children over and over. In the end I stuck with items instead.
You also get the successive amounts of gold for having children even though you wiped the early ones!
Daniel.