(Warning: I may have already told this story before. However, I'm not sure, and I couldn't find any evidence that I might have. So I'm running with it again. And you can't stop me. Muahahaha.)
Once upon a time, a teacher told my class, "You have to be a sick, twisted person to be a writer. You can't help it. Because writers have to torture their characters." He wasn't kidding. Basically, to be a writer, you need to create characters. Give birth to them. Learn them. Love them. Then you need to kick them in the stomach on a regular basis.
I can't help but agree. We're twisted.
I have a special feeling for each of my characters, especially my MCs. I know their histories, their wishes, what makes them tick. We're close. And then I do awful, awful things to them. For Amira, I know her history, what she wants most, what she hates and fears the most. What else have I done to her? Well, her grandfather gets murdered, she's almost executed, she's exiled, she goes to war, she's almost murdered too. And I'm not done yet. I'm planning on amping this up in the next round of revisions.
You're the same way. Admit it. You know your MCs, probably back to front and inside-out, and you put them in dangerous situations, untenable situations, risky situations. You find out what they want and put as many roadblocks between them as you possibly can.
That's perfectly okay. It's what writers do.
Practice this sentence with me: "I am a genius of tremendous and remarkable power and evil. I am out to control my universe. Muahahahaha." (Yes, the evil laugh is obligatory.)
I know you love your characters. I'm sure you do. But, that doesn't mean you don't have to make them suffer. Think of it this way, it'll just make it all the sweeter for them when everything comes 'round right.
How goes your malicious wickedness, fellow genius of remarkable evil and power? Have you ever experienced difficulty working acts of evil against your characters? Is that hard for you?