Using the same logic that allows spells like Nullify to work. How can you prevent a spell from resolving if it is already finished? You can't. But since it has not finished yet, you can still affect it with things like counterspells and incapacitate to interrupt it. I believe the wording in the rules is to indicate that you are now committed to the action, just like with the declare attack step, and that's all. You've begun casting and are past the point of no return, but you aren't finished with the spell until step 3 ends.
Granted, there's nothing that says incapacitate works this way, but it is not an illogical interpretation like you seem to think. We know that it does affect the steps of combat, which work similar to the steps of casting a spell, and we know that there is time to still stop a spell from being cast after step 1 because spells like nullify are able to.
In the end, I think we are in agreement about steps 1 and 5 of combat, and step 1 of spell casting all being affected. I could certainly see things ending there. But, I still think it's possible that steps 3 and 4 of combat, and step 3 of spellcasting could be affected as well.