Although Cyclops and Cap have gone through a similar situation where they both did things against their will in a moment where they were not themselves by either Phoenix or Kobik the difference is what led both to this situation.
Cyclops while still believing in Xavier's dream the circumstances led him to be more extremist to ensure the survival of the mutants. No matter how people say he tried to dominate the world, this is not true. And if he had to do it all over again, he would do it to save mutants.
In the case of Cap is different Kobik changed the character in a way that this Steve is not the character we know. The real Steve would not compromise his values even before the end of the world as we saw in Time Runs Out. If he could, he would undo the evil he did when he was changed.
Now regarding consequences Steve is an Avenger and Scott is a hated and feared mutant even though Cyclops has saved the world almost as often as Cap so it is obvious that the treatment that both will receive will be different.
The best proof of this is that Scott was arrested after AvX and hunted down as a terrorist by Shield. Now about Cap doubt that something similar happens although do not think citizens will forget it so easily.
In fact Cyclops himself said that the US government would never allow him to be heard on trial. All they could do was either disappear with him or bury him in a prison. The same will happen with Cap the American government can not judge him because during the testimony it would be of general knowledge that the American government and Shield are responsible for the creation of Kobik so they will let Steve go and invent some history about Hydra control him (which in a way is also true).