Sin is the transgression of the law. – 1 John 3:4

Whatever is not of faith is sin – Romans 14:23;

All unrighteousness is sin – 1 John 5:17;

To know what good you should do and then not do it, it is sin- James 4:17

Finally, I assume you hold to this as well; there so many diverse ways to commit sin that they can’t even be numbered and include sins in thought, word and deed, failing to observe the commandments, and not continuing in the faith. – Mosiah 4:29-30?

CONSEQUENCES OF SIN:

It is so true and I agree that there are surely natural or temporal consequences to sin and bad choices.  Smoking leads to cancer…  Immorality leads to STDs… Lying leads to a bad reputation… and so on. 
 
You also mentioned there are spiritual consequences to sin as well.  Here are some I found.  Would you agree with these as well?

Consequences or wages of sin is death – Romans 6:23
Fearful, unbelievers, corrupt, murderers, liars and so forth end up in the lake that burns w/ fire. – Revelation 21:8
ALSO, in the Mormon canon: Liars will be thrust into hell. – 2 Nephi 9:34
He who sins and does not repent will be cast out – D&C 42:28
Without repenting, the light you have will be taken away – D&C 1:33
If you fail to repent before you die, the Spirit of Lord withdraws from you and the devil seals you to himself – Alma 34:35.

 
 
Here is what I think you mean, and please correct me if I am misunderstanding you:  if we repent, we can be forgiven and avoid the  spiritual consequences of sin?  If we repent, we are not “in” sin anymore?  Also by truly repenting, we are saved from our sins and Christ helps us remove the desire to be disobedient?  Is that what you mean? 

Alma 11:37 is from the middle of the “saved in your sins” vs “saved from your sins” discussion. We cannot be saved in our sins, our sins being the willful disobedience to God. We can be saved from our sins, that is, Christ can help us remove the willful disobedience part from ourselves through repentance.

Deuteronomy 32:4 “He is the Rock, his work is perfect: for all his ways are judgment: a God of truth and without iniquity, just and right is he.”

Psalm 5:4 “For thou [art] not a God that hath pleasure in wickedness: neither shall evil dwell with thee.”

I think the part that confused me is when you said, “It isn’t so much that God will punish those who break commandments.”  Perhaps I just misunderstood your point.  I always thought that the LDS believe God does punish sinners/commandment breakers; at least that is what I got from the Book of Mormon. 
 
What do you suppose is God’s standard for us?  Do you hold to Alma 11:37 as being true?