This story does set up the reason for the conflict but looking at it closer,the reason seems to be Cyclops paranoia and xenophobic tendencies causing the fight. Lately he’s been so Pro-Mutant and ant-anything else it’s like he’s been studying Magneto from the 70’s. He’s acting out of character. First he makes this statement to Wolverine in Schism that he had to know would start a fight, when they were in the middle of a larger fight. ANd the result was the team was split. Now he fires on Captain America, and due to his position in the government, that could be sen as an act of war or terrorism. That whole “This is a Mutant problem. We’ll handle it.” sums it up nicely. His irrational position on this has caused him to start a fight he can’t possibly win and alienate people who could actually help. He started this, now he’s going to have to deal with it.