I think they thought the same way that Lana Parrilla did about it. In one interview, she referred to Regina's relationship with Graham as fun and flirty, while Jamie Dornan in interviews for the same episode referred to it as sad and horrific. The showrunners were clearly pushing Parrilla's interpretation. I do think they go with the she's hot, so who wouldn't be happy to hit that? mentality, while Dornan was very obviously aware that his character would not have been cool with being a sex slave just because his mistress was hot. Jane Espenson was the only writer on the show to ever acknowledge that it was rape.
Keep in mind that these are the same writers who thought everyone would be super fine with Regina and Robin getting it on in the crypt while his wife lay in a cursed sleep not far away. True Love y'all. I think that they have trouble separating fantasy (thoughts and dreams) from fantasy (fiction). A fantasy show is a story and it has things like magic and curses and crazy worlds, but the people who inhabit those worlds aren't free from emotion or feelings. Cheating on your spouse in a fantasy world that still has things like marriage vows isn't any different than doing it in the real world. There is no absolution in it being a fantasy.
Sometimes the method of an action is different because of the fantastic aspects, but it still results in the same feelings and emotions for those being subjected to it. In our world we can't pull out someone's heart and control them into having sex with us, but we could roofie them into submission. Or we could simply tie them down and forcibly commit rape. The psychological effects on the victim will still be the same afterwards.
Poor Graham had it worse in the Enchanted Forest in that he knew what was happening, hated it and still was magically compelled to do it. In Storybrooke, he felt wrong about it, but at least he didn't know why. And he did finally say no when Emma's appearance allowed the curse to diminish some of its effects on him and he was able to break free a bit. That they had Regina kill him after he rejected her made it about 80 million times worse because again, this is not an action that is unique to a fantasy world, but something that happens all the time in the real world. Just because she could do it by squeezing his heart instead of stabbing him through the heart with a knife does not somehow make it less real.