I think Season 3 tilted towards Emma and Hook in such an obvious way that they intended them to stay together without network interference. Albeit, they clearly enjoyed and found it easier to write for Hook than Emma, so it's possible they kept the relationship to ensure Hook had a reason to be there.
I think overall, that was just how A&E wrote, and Captain Swan wasn't necessarily a target. Look at Rumbelle, a coupling they clearly thought was true love. Rumbelle got a "romantic" engagement and wedding but we found out Rumple gave her a fake dagger and he murdered Zelena behind her back. Rumbelle had a "romantic" honeymoon complete with a Beauty and the Beast dance, and then we saw Rumple discovering the Hat Box. The Writers' concept of writing for a couple they loved was creating obstacles and creating angst so that the two characters realized how much they love one another. I find it hard to believe the network cared about keeping Rumbelle together since it was actually damaging to "Beauty and the Beast". I doubt beyond Season 4, ABC cared too much about this show overall since it was basically maintaining its small base core audience.
Of course, it's hard to trust anything they say but,
Of course, this was before the couple became "happy" aka boring. I think after 3B when Hook and Emma both shared the same feeling, it just became their usual inability to write good, human stories for established couples which resulted in the bad writing for CS. If they had wanted to break them up, they could have easily done what they did with Regina and Robin Hood.