Why is spontaneous emission neglected in standard discussions of the two-level system? When discussing two-level systems, spontaneous emission is often neglected `until later'. However, when discussed later, the two-level system is no longer discussed. For example, see Straten and Metcalf.
Why in simple descriptions of the two-level system can spontaneous emission be safely ignored? I think it is simply assumed that the Rabi frequency is far greater than the spontaneous emission rate? Or, to put another way, the lifetime of the excited state is very long lived.
 A: This is a good and nontrivial question.
The short flippant answer to why spontaneous emission can be ignored is because we ignore it.
What I mean by this is that there are experimental regimes where we can have what you say, either very high Rabi frequencies or very long lifetimes, which are both conceptual statements of the mathematical condition $\Omega \gg \gamma$. In those conditions the predictions from ignoring spontaneous emission match observation really well.
But in my view, ignoring spontaneous emission is more of a learning exercise: you do it to clear away extraneous detail and get to the heart of how the system behaves, namely Rabi flopping. The effects of spontaneous emission are secondary in some sense: you want to see that a light field can transfer population between two levels, and you want to know how fast. The decay due to spontaneous emission is just clutter. Imagine a spherical cow.
There's also a deeper issue here: you'll never get spontaneous emission out of any theory that treats the EM field classically but the atom quantum-ly. Instead you have to quantize the EM field as well; and then the combined atom+field system is, in a real sense, infinitely far from a two-level system, since the states are now $|g,n+1\rangle$ and $|e,n\rangle$ for any $n \geq 0$ (and also $|g,0\rangle$), where the second label indicates the number of photons in the relevant mode (which I incidentally assumed there was only one of).
