In a "Hypothesis Contrary to Fact" (also known as a speculative fallacy), the hypothesis is usually based on something in the past and it is not factual. And the illogical argument goes something like this: If 'X' would have happened, then we would not be in 'Y' situation. This is like confusing what might have been with what should have been. Another example: If George W. Bush wouldn't have become president, the country would be much better off today. One could argue points to support this, but it is impossible to know for sure. This kind of speculative argument often involves a speculation in which we suppose that a different past event would have lead to a specific, different future. It is fallacious because it involves a prediction that we can not prove for sure.
The premise of the story is that if the animals could run the farm they would be better off than under Farmer Jones. This is a legitimate hypothesis going forward. Of course, it resulted in corruption and oppression just the same. Readers of the story can speculate that if Snowball had remained in control things would have worked out. But again, this is speculative: a hypothesis contrary to what actually happened.
In Chapter 5, we have an example of hypothesis contrary to fact. Snowball and Napoleon begin to argue over everything. Snowball wants to encourage rebellion in other farms. Napoleon wants to focus on their own farm. The biggest argument is over the windmill. Snowball thinks it will make them more energy-independent. Napoleon claimed to be against the idea. The narrator claims that if Napoleon and Snowball could have gotten along, things would have turned out well:
It had come to be accepted that the pigs, who were manifestly cleverer than the other animals, should decide all questions of farm policy, though their decisions had to be ratified by a majority vote. This arrangement would have worked well enough if it had not been for the disputes between Snowball and Napoleon. (Chapter 5)
The decision of having the pigs run the farm "would have worked well enough?" There is no way to know whether this would have resulted in a peaceful Animal Farm. If history is any lesson, power corrupts and absolute power corrupts absolutely. There is no way to know for sure if a joint Napoleon/Snowball ruled farm would have been successful and just for all the animals. Likewise, there is no way to know if a farm run solely by Snowball would be any better. The power might have corrupted him as well. It seems that Snowball would have been the better ruler, but it is speculative. Therefore, it is a hypothesis contrary to fact.