The link you gave suggests these two things:
1. Don't transport any fish from one body of water to another, which can help spread whirling disease.
2. Don't dispose of fish entrails or other by-products into any body of water.
The key issue is transport and cross contaminate water - that's why they are so careful to educate people about washing their boats, waders, boots, etc. before dropping in to another water body. Transfer of plants, fish, entrails, mud, etc. from one body of water to another is thought to be a mode of cross-contaminating waters.
I'd suggest that the disposal of entrails is the same, and the language is either not clarified well enough in the regulations, or it's mentioned because of trying to get the population in the habit across the board of take stuff out of the water, don't put it back in. But taking original organic matter from a body of water and disposing the same back into the same body of water should not increase whirling disease risk in that body of water.
In the backcountry of Yellowstone Park, they are concerned not only about attracting grizzly bears to buried entrails piles, but also in cross contaminating water bodies with whirling and New Zealand Mud Snails. Their policies include:
"When fish cleaning and disposal areas are not provided, dispose of fish entrails by puncturing the air bladder and dropping into deep water. Do not clean fish in backcountry campsites."
"Drain livewells and clean fish ONLY near the same body of water in which they were caught."