What role does Boxer play on the farm?Why does Napoleon seem to feel threatened by him?
In what ways might one view the betrayal of Boxer as an alternative climax of the novel (if we consider Napoleon's banishment of Snowball and the pigs' initial consolidation of power as the true climax)?
Boxer is the farm workhorse. He is large, strong, and exceptionally loyal to the cause. His fault lies in his own child-like innocence, and his propensity to believe anything that anyone says. Despite his naivete, however, if Boxer were to report to other animals exactly how scheming and evil the pigs were, they know that they could easily be destroyed.
This fact is why Boxer is viewed as a threat, despite being an ally, and why his eventual fate comes about. While the betrayal of Boxer is not, as you said, the true climax, one could indeed construe this event in such a way that it legitimizes as an alternative climax. After all, the betrayal of Boxer is nearly equal in importance to the banishment of Snowball, politically speaking.
Boxer represents naive and uncritical loyalty to the new regime. He sees how life for the animals improves initially and is prepared to work as hard as he can to bring the ideals of the revolution to fruition. His intelligence is limited, however, and he is too trusting and naive, stupid even, to see the reality of corruption infecting the pigs' regime. On the other hand, his naivety also leads to him openly expressing his puzzlement over certain things and this is potentially dangerous for the pigs as it might lead to other more intelligent animals beginning to question what is happening. This, together with Boxer's enormous strength, is what makes him a threat to the pigs: they desperately need him for his enormous capacity for work and example but, if that strength were to be turned against them because he unwittingly alerted the rest of the animals to their corruption, then their regime would be finished.
As regards the second part of your question, I don't have much space left but I think I take your point about the climax. I have never liked the novel's ending and, now that you have mentioned it, I do think something better could have been fashioned out of Boxer's fate. In a sense he is the key character in the story, the tragic victim destroyed by his very loyalty, just as ordinary, hardworking people are so often destroyed by tyrannical governments.