Microsoft can secure the exclusivity by cofunding the development and marketing for the sequel(s) like they did with GoW (with EA getting primary investor status, meaning they get paid first before anyone else) . Now before people get up in arms with "No way will EA leave all dat PS4 money!" EA is in a win/win with this deal: if the game tanks/doesnt hit the projected numbers, Microsoft takes the hit since EA will get paid off first and won't have to front all the capital for game, the game does well EA reaps the profits. That kind of deal off loads most of the risk to Microsoft and allows EA to use its development dollars on IP that the company itself owns.
One thing that a lot of people don't understand is that companies do not like risk, which is why you see sequels and reboots. If a company can do anything to reduce its exposure to risk and still maintain a healthy profit it will do it.