They did have to mind-wipe Cap because he wouldn't even consider putting all options on the table. It'd have been different if he was offering some other alternatives but he wasn't. With Cap on the team they wouldn't have even survived the Latverian incursion.
The built the bombs "just in case" but they had been looking for other ways to deal with incursions. They named a bunch of things they had been come up with during the New York Incursion. Since then they've been studying other worlds to find solutions.
The entire time Namor has been mocking them for holding out hope that they could find another way.