If you had that much yeast in your secondary, I'd think you didn't leave it long enough in primary for the yeast to complete the ferment. Not much to do about that now.
Autolysis is a product of too much heat. When you have a few hundred gallons of beer in a conical fermenter, the yeast drop out just like they do in your bucket or carboy but there is so much more yeast and being in that conical, they are all jammed together. The yeast give off a little heat. No problem in your carboy but when you have 10 gallons of dormant yeast in the bottom of the big conical, they get too hot and the yeast die and begin to decompose. That's autolysis. You should have nothing to worry about.