I'll answer my beliefs as best I can. I do so with a couple of caveats. First, I am not a spokesman for the LDS faith. I am just a member, and not even in a leadership position (well I'm a Ward Clerk, but that mainly means I am mainly a glorified gopher). Second, I am not a theologian. I read and study, probably more than a lot of people, but I don't have any formal training outside of church. I am constantly learning new things, incorporating new ideas, and having new insights. In short, I don't know it all, and can only speak for myself.
Additionally I find that often terms that are in common LDS use are misunderstood by those who are not LDS, and we sometimes misunderstand what is being said by those of other faiths. I will try and omit "jargon" or at least clarify it when I feel it is necessary.
With that out of the way, I think the best way to answer the question is to address how I see the atonement, and how it applies in my life.
I have struggled to really understand the atonement, and my appreciation of it has deepened over the years as I have begun to understand its deeper meanings. At its root I believe the atonement is the bridge between mercy and justice.
God is just. He gives us laws for our own good, to keep us safe, and guide us to be better than we are. It is these sins that make us unclean and unable to return to the presence of God. As we all sin there needed to be a way to cleanse ourselves. Thus the atonement.
Second, and perhaps more important, is the ability to wash ourselves clean of sin. There really are two parts to this. There is the cleansing of sin. If we have transgressed the law, the law must be satisfied. This is the justice part of the equation. By Christ descending below them all, yet being guiltless himself, he took all our sins upon himself in an infinite sacrifice. In this the law can be satisfied (justice), but we can be saved from our sins (mercy).
This is not automatic though. We must take Christ's name upon ourselves. We must consistently repent of our sins and ask for his forgiveness. As we do this He grants that His sacrifice applies and we are washed clean. This is not a one time thing. There is no moment you are "saved", it is a process. It is a day-in day-out effort to stay close to Him. As we do this we are refined, and our thoughts and actions become closer and closer to His will. Were we able in this life (and we are not) to live perfectly, we would have the ability to understand his mind fully. As it stands though, we can see and understand more and more as we study, pray and repent.
This is some of the confusion that I think is often brought up about Mormons becoming gods and planets and all that. The real story is really just a continuation of the above after this life. As we continue to grow closer in thought and action to Christ and God, we eventually "become one with them". In our theology, this is one in mind and purpose, able to act in his name. Again, we do not become God, or replace or even equal Him. Rather we become like Him knowing His will, with our minds in concert with His, and having the ability to act for Him.
Please understand I have really distilled this down. No matter how I state it, it feels inadequate to communicate the fullness of the concept. Frankly, I don't believe that I fully comprehend it.
A few things that I noted I'll address directly:
- "God sees Jesus instead of us when He looks at us." No, He sees us as we are.
- "God is allergic to sin." Wouldn't that make him imperfect? No, we would not want to be in His presence in a sinful state.
- "Since God is infinite, He is infinitely offended by the slightest of our sins" No. I have some tangential thoughts on your article, but I think you dealt with it well.
- "God poured out His wrath on Jesus on the cross." I have to say, this one baffles me on every level. From a Trinitarian standpoint isn't that essentially flogging Himself? No, the pain was not caused by God, though he allowed it. Again, this is a much bigger topic than this article.