I would say the atoms in your body are just as sacred as the rest of the universe, its the combination that makes you unique that sets human beings apart.
If you're coming from a religious 'spirit of god' perspective, your question will expose one of the many hypocrisies that exist when trying to marry up scientific reason with religious faith. But I guess they will say the 'soul' leaves the body at death, which is when it loses sanctity.
From a more physical perspective I'd imagine the concept of time must enter into how sacred humans are; the matter of our bodies having once existed in star dust and will end up as who knows what. Human consiousness (which I would say is a more narrow definition that just human life) would be sacred in that its a point along this journey that becomes aware of events around its own existence, and wonders.
Good question, but to summize my answers to your many subquestions:
Is there anything sacred about the atoms, molecules, DNA or cells that make up the human body?
Not individually, but together in a human, yes.
If so, at what point of complexity does our matter acquire sanctity?
Consciousness? Or when surrounding humans consider potential life precious, such as embryos. I think this hints at sanctity not being a very objective term.
Atomic, molecular, genetic or cellular?
As above, only in combination.
Or does that sanctity relate only to vital organs and their constituents?
Does our matter suddenly lose its sanctity when expelled from the human body?
Yes, at least for a years until it can be reabsorbed into our bodies as food.
Or would that depend on its potential importance to other humans?
Sperm? Yes many would consider this sacred, due to its potential. Subjective term given by humans though.
And does the matter that makes up the human corpse retain its sanctity? Even after it has been ingested by worms?
Being ingested with worms helps it towards being sacred again as it gets reintroduced into the food chain?
Anyhow, nice question, I'll be interested in what you think the answers could be.