I have noticed that kiling iron golems will cause a major decrease in reputation if the killed golem belonged to a nearby village. Dealing the knockout blow is sure to cause this, but I am wondering if non-player damage (such as environmental) would trigger this, as I used NBT Explorer to change my reputation in a village to 10, waited for several golems to die from a nearby automated iron farm, and when I rechecked the reputation value, it showed 1! If environmental damage killing an iron golem causes you to lose reputation in a village, that could spell the doom of (most) iron farms!
EDIT: Sorry if I have bad english! English is not my mother language!
I'm thinking that if you are too close to the iron golem when it does, the village thinks you did it. Perhaps you could try to be more than 16 blocks away from where the golems die in your farm and see what happens? If this doesn't work, maybe try 32 blocks away.
If all else fails, you can simply make a second village away from the main one (probably by transporting villagers) to build your farm, so that you won't need to worry about reputation (reputation from one village doesn't effect others.)