Physical implications of the simple harmonic oscillator quantum mechanical solutions
However, to reach this state from, for example, x=0 in the n=2 energy
  level it must pass through a node.


To start, ask yourself: "What should pass through a node?" The answer is: it is the probability that "passes through the nodes", not atoms (or, I should better even say nuclei). Probability is just a mathematical quantity ant the zero value is allowed for it, so there is nothing to worry about. Yes, quantum harmonic oscillator has some forbidden regions of displacement from the equilibrium. But it can also penetrate into classically forbidden regions. Quantum world is weird.

The root of this (and most of the other) apparent quantum paradoxes is the classical way of thinking: you think that you have some funky quantum balls on a funky quantum spring out there, but you don't. Quantum harmonic oscillator is a quantum system that essentially has the Hamiltonian similar in its form to the Hamiltonian of a classical harmonic oscillator. And this is it. No balls, no springs, just a similar Hamiltonian.



It should be mentioned as well that atoms (again, more precisely, nuclei) are not vibrating in molecules even in a classical sense: their motion can be only approximately separated into vibrational and rotational ones. Besides, the vibrational motion can only approximately be treated as being harmonic.