It's completely intended. The protagonist is a UEF service member because that allows us to tell the story we wanted to tell: a formal inverse of Age of Aquarius that begins in a state of enlightened grace and then must grapple with the needs of war and the difficulties of a morally gray universe. Where Bei reunites and saves his broken family, Laporte must find meaning and purpose in the midst of an enormous shattering.
We don't really view the two factions as protagonist and antagonist. They're two characters with rival agendas and differing conceptions of morality, but they both have good intentions for humanity. We'd be very disappointed if there weren't people rooting for both sides.
More directly put: the developers don't have a team, and if everyone agreed one side had the clear moral high ground, we wouldn't be doing our jobs.
