I have two characters that I'm writing about, and I'm trying to write the conflict in a way that makes sense. They are both aliens - one male, the other female - from separate alien races, who are friends yet secretly have feelings for each other with neither knowing about the other's. The conflict is that the female alien is a doctor and hates violence (she is partially inspired by Mercy from Overwatch) because she grew up during a war that led to experiences in her childhood including seeing horrible deaths, losing her home and her left arm (thank God she's wealthy and future cybernetics technology). She finds out that her friend is a solider in the army - he's an engineer in his civilian job, but is also a combat engineer who has seen action and killed people in the line of duty. He enjoys being the army somewhat because he was a sickly child who had to work hard to overcome being physically frail - which he did ala Teddy Roosevelt (look him up) - and being in the army is this, a way of helping people and he's got something he's good at (she doesn't know those reasons). He's also not a solider in the army that subjugated her people - he's actually a solider in the army that liberated them - but her abhorrence of violence, seeing him kill someone (admittedly who was trying to hurt innocent people), his past and their feelings for each other make this a touchy issue. How would this kind of conflict play out in an engaging or realistic way and what would be a good way to resolve it? (my idea for the resolution is that she visits a war memorial, sees the sacrifices he and others like him face and learns about his past).
how do you rationalise the different alien races having feelings for each other... that's like bestiality
What I'd suggest is to have each of them confronted with a situation where their philosophy isn't enough, and they see the merits of the other's outlook. For example, maybe she shows mercy to someone who really doesn't deserve it, which puts innocent people in danger until he takes more decisive action to end the threat. Or maybe they're ambushed by bandits and he can't see a way they could fight their way out, but the bandit leader lets them go after recognising her as the one who saved his brother's life.
I think of it the same way it's done in the franchises Mass Effect or Star Wars; there humans and aliens, or aliens and other aliens, find love, sex or relationships and it isn't bestiality. Canon examples of couples in Mass Effect include asari ( http://masseffect.wikia.com/wiki/Asari ) and elcor ( http://masseffect.wikia.com/wiki/Elcor ), asari and krogan ( http://masseffect.wikia.com/wiki/Krogan ) and turian ( http://masseffect.wikia.com/wiki/Turian ) and quarian ( http://masseffect.wikia.com/wiki/Quarian ). So leaving aside the question of "aliens from different races having feelings for each other" (hasn't stopped writers doing all those human-on-alien relationships), please feel free to share opinions on my story arc.
On the arc itself I'd say that the feminine doctor who hates war falling for the masculine soldier who feels it is justified is a colossal cliche
This is a typical situation and it's popped up a lot in romances -- brutal warrior, prairie school teacher. Brutal pirate, wenchy rich girl. All of the women hated violence. Usually it came down to a heightened scene where the women had to use violence to save a child or themselves or both and being put on the spot learned you can't be passive with a violet enemy. I think make it more subtle -- less so opposite or you probably will be writing a scene like this. Maybe change up the flavor of the conflict and you find out she's only using the army angle because she's afraid of a long term relationship or she's wary about the differences in them or maybe she's worried about her replaced arm and feels less womanly.
A good start would be to actually have opposing view points. They don't. They just have forced backstories that don't even make sense. You have a doctor who doesn't understand reality, despite living through a war so her motives are impossible to take seriously. Then you have the soldier who... actually you don't mention where his viewpoint is. A second place to go would be not to be so overly simple with your material. You haven't described any real nuance with the situation. It's really just a whole lot of "I don't like killing and you just killed someone." You're not arguing the pros and cons of anything. Finally, what does learning about his past accomplish? That doesn't accomplish anything in resolving a different point of view. Unless she's completely unappreciative of anything the military does, in which case, why are they even in the same room together? But even more important, this resolution tells me nothing. A good example of an opposing viewpoint would be with reconstruction efforts. War does not end with a pretty bow on it. You have to rebuild resources and supply lines that war destroyed. You have to deal with shortages. Often times you have long periods of instability where civilians fight each other. So you could have it where these two met during the war while he's liberating. She acknowledges the need for this army to come in and help, but she doesn't like the idea that this army has chosen to stay as an occupying force. An occupying army, even one with good intentions, can be very difficult. Sometimes they break what they're trying to fix by standing in the way of meaningful reconstruction efforts. Sometimes they even unintentionally escalate violence. But there's also another side. Without the occupying force, the country is vulnerable to being seized by warring factions and neighboring countries. While the soldier doesn't actually know if that will happen or not, it's not a risk they want to take. And there can be an argument made that violence would be worse without them. And that is now an actual opposing viewpoint. Now it has a purpose. Now, you're actually arguing the pros and cons of a very nuanced situation where there is no good solution. And how do you resolve this? You don't. People never resolve differences like that. They simply make peace with it.
@SnapWrex1 -- I think what's most interesting and gives you options is that one of your main characters is a doctor (trying to help and save people) and one is a solider (trying to kill and liberate the people even if he's not primarily there to fight). You could give him PTSD and the doctor could want to save him from this, from himself. You could have him get hurt in the fighting and she has to try and save him. You could make it friendly fire for some added conflict. Or you could have her have to take care of someone he hurt. Again, I like the idea of friendly fire here, but it's totally up to you. By doing this sort of thing their worlds really meet face to face. I think you have a good set up that you could take in many directions, but I would have the worlds (meaning their views) collide on some scale. It could be very interesting. Good luck with this one. I like the set up you've got.
If you really want to switch up the stereotypes, it would be more meaningful to instead do a soldier who hates war and reluctantly fights out of necessity while trying to reduce killing, and a doctor whose experience with violence- rather than making them hate about war- has helped them be more tolerant of it based on the idea that violence is a constant. Or something to that effect.