The myth of Silent Hill's religion states that before their god was brought about, theses things happened:
"A man offered a serpent to the sun and prayed for salvation.
A woman offered a reed to the sun and asked for joy.
Feeling pity for the sadness that had over run the earth,
God was born from these two people."
Now, if you want to take the myth at face value, it just basically says that god felt humans were so pitiful, she came to earth to bring them happiness. That's one interpretation. However, I believe that the despair leading to pity is a misconception created by the cult. We saw what happened with the two gods born from hate and pain; they were monsterous and violent, things that this merciful god the myths speak of would never be.
So let's look at this again. Maybe god didn't come from the pity she had for humankind; perhaps what the myth is really trying to say is that the vessel meant to hold god (the woman) felt love and joy from this man, thus she could properly birth a kind and merciful god. Now, let's look at Heather/Alessa. They were both made to birth god, and twice, they fail at it. Why is that? They tried to make her birth it the wrong way, so the god came out wrong. What she is really meant to do is birth the god with love in her heart. This doesn't happen; she fails; she must try again. Simple as that.
I believe Stanley has a similar role; he's there to make sure that Heather has a happy life filled with love and joy. If you believe that Stanley is Andy from Silent Hill: Play Novel, then it shows that he can be incarnated there just as Alessa can, and he's there to watch over her and make sure she's happy. This is why he loves Heather/Alessa so much; it's a function that he is meant to perform and he does it quite happily. That is, until he realizes that Heather or one of her incarnations is not going to birth the god properly. When this happens, he goes into a sort of double destruct mode, and he wants to kill them both to try again. This is why Stanley acts the way he does when we read is journals. He's become incredibly self destructive, and it's evident that he also wants Heather to go down with him. They can try again, hope to cult doesn't interfer, and properly birth a caring god.
This is probably why the cult shut him up into Brookhaven Hospital. He was obsessive with Alessa, but it was his nature to do so. He also did not agree with the cult's way of bringing about god. The cult didn't want him to interfere, realizing that he would want to kill Alessa if she was going to birth god the way they wanted, so they lock him up. Heather ended up going to the Hospital anyways though, and 'met' Stanley. In the end, Leonard killed him, either in a fit or because he realized that the Stan man wanted to kill her. Leonard probably screwed up the cycle of the reed woman and the serpant man by doing this, which may be why Heather's acting so screwed up no matter what ending you get. Now I figure she'll instinctivly try and kill herself to right the cycle or go crazy. You decide. :D
In conclusion, I think Heather was made to birth god, and Stanley was made to make sure god was birthed right: with lots of lurv. If something goes wrong, it's their duty to make sure they die. The end. XP
Comment any thoughts, or complaints you have with my theory.