People often assume that Morgana is the personification of evil. But I don't think that is correct.
If you read Kayle's bio, you see that she is ruthless on judging and punishing others; she is an angel who acts on behalf of the gods. While Morgana decided to abandon those gods for a reason we don't know.

To support my arguments here are Morgana's quotes:
"Feel my pain."
"Share my torment."
"I'll have my revenge."
"You too will be judged."

Now Kayle's quotes:
"Your time has come."
"An eye for an eye."
"Who's next?"

So from the quotes we see that Kayle has no compassion on judging others, while Morgana's quotes clearly says that something was done to her, or maybe to someone she loved; and that's why she is in pain, and she wants revenge. I think the strongest quote is "You too will be judged", which i think that's the reason of her suffering.

I read once a fan made story about a forbidden relationship of Morgana with a mortal, who was then slain by Kayle because angels should not fall in love. And well afterwards Morgana cursed kayle and became a fallen angel .

Here is the link: http://www.fanfiction.net/s/6393022/1/Viridian_Kayle

I think their story should be deeper on season 2.

If you read one of the JoJ, you'll realize that Morgana seeks freedom from the tyranny of angels. Most likely, the angels, in her POV, had a hypocritcal form of light. As you said, i think some form of misguided justice, resulting a lost of a loved one or something just as tramatic. She was never had personification of evil in nature, but she is willing to do evil things if it meant ending the cycle.

Morgana is more... malicious seeming to me than outright evil. Perhaps her Ends aren't necessarily bad, but what she's doing to get there aren't nice things at all really. There's also the fact that according to her quotes I'm pretty sure all of her abilities are a way to force someone else to share in the constant agony of her condition, so again while not necessarily evil Morgana is far from a shining beacon or Anti Hero.

They both represent extremes much like Demacia and Noxus do.

Kayle is what happens when a person is too self righteous and views the world in black/white. Morgana can be seen as what happens when you have too much freedom and disregard the law.

I'd say it is very much a point of view question. What you suggest is very much a possible scenario. Lastly, Riot seems to make a point out of both demonstrating the good/evil stereotypes, but preserve a large moral grey zone and prevent there from being truely GOOD or EVIL sides. Some people are obviously nasty, amoral people (Veigar, Vlad, Warwick etc.), but the seemingly good ones (Garen/lux for instance) are not that good after all (see Lux' judgement.). So yeah, it's probably very much a point of view thing.

There are villains who refuse to win by any means less than honorable, and there are heros who will "stop at nothing" to bring down some evil force. I've always thought the difference between good and evil is now how they fight but why they fight: the preservation of self vs the preservation of others.

But to what extend does the end justify the means? And is it preservation of self or preservation of others when a system/state sacrifices hundreds and brainwash/oppress/indoctrinate thousands to maintain itself?

The latter case can be said to be the case with angels and Demacia alike.

This is a classic argument in psychology. Behaviorists believe that, regardless of the purpose or motivation, the how is more important that the why. This is because the how is the only observable, concrete data you have. If someone says "I'm trying to save the world" then blows up a preschool, then they are still seen as "evil" even if they are motivated by some sense of justice or "good". In this sense, Morganna is driven by revenge and an intense hate as well as fighting for a paradigm shift against the oppressive angels, but that wouldn't be what mattered. She fights with dark arts that focus on binding, corruption, and causing pain. In this sense she is "evil". On the other hand, Kayle's fighting style has some damaging skills, but it has equal parts healing and protective qualities. Since she saves her allies, she is seen as more "good". All in all, though, it does come down to a combination of motivations and behaviors. Morganna owns a bakery chain for crying out loud, so I wouldn't call her "evil".

I'm pretty sure Morgana is the good one:
her q: binds an enemy, preventing them from meleeing one of her allies.
her w: places a protective ward on the ground, discouraging foes from approaching
her e: protects her target from all ill effects, except physical damage
her r: is retribution for those who would attack her, allowing her allies to escape after a mere 2.5 seconds.

Compared to Kayle:
her q: blasts an opponent slowing them and making them take more damage from Kayle, clearly an initiating move.
her w: revitalizes an ally, giving health and movement speed so that they can charge in and beat the **** out of someone (synergizes with q)
her e: allows her to reign down destruction from great distances; a cowardly yet destructive move if ever there was one.
her r: MY ALLY CAN BEAT THE **** OUT OF YOU WITHOUT ANY FEAR OF PUNISHMENT!

Kayle is clearly the evil force intent on destruction, where as Morgana is all about protecting her allies and her bakery from the forces of evil (she just happens to use black magic).

I'm a fan of your rose colored glasses good sir, you must be quite the fan of baked goods.