Let us write the equation in state-space form
\begin{equation}
\frac{d}{dt}\begin{bmatrix}x_{1}(t)\\
x_{2}(t)
\end{bmatrix}+\begin{bmatrix}\eta/2 & -\omega\\
\omega & \eta/2
\end{bmatrix}\begin{bmatrix}x_{1}(t)\\
x_{2}(t)
\end{bmatrix}=0 \tag1
\end{equation}
where the natural frequency is $\omega \triangleq \sqrt{1-\eta^2/4}$. It is easy to verify that the characteristic polynomial is indeed $p(\lambda) = \lambda^2 + \eta \lambda + 1$ by construction. When $\eta \ll 1$, we have $\omega \approx 1$, so the solution can always be approximated to great accuracy as
\begin{equation}
\begin{bmatrix}x_{1}(t)\\
x_{2}(t)
\end{bmatrix}=\exp\left(-t\begin{bmatrix}0 & -1\\
1 & 0
\end{bmatrix}\right)\begin{bmatrix}y_{1}\\
y_{2}
\end{bmatrix}\tag2
\end{equation}
with $y_{1}=x_{1}(0), y_{2}=x_{2}(0)$. Indeed this is the exact solution when $\eta=0$. Now, with a finite $\eta$, this solution is not completely correct, so we let $y_{1},y_{2}$ vary with time to yield
\begin{equation}
\begin{bmatrix}x_{1}(t)\\
x_{2}(t)
\end{bmatrix}=\exp\left(-t\begin{bmatrix}0 & -1\\
1 & 0
\end{bmatrix}\right)\begin{bmatrix}y_{1}(t)\\
y_{2}(t)
\end{bmatrix},\tag3
\end{equation}
with $y_{1}(0)=x_{1}(0)$, $y_{2}(0)=x_{2}(0)$. These variables can be intuitively understood as “corrections” to the initial guess above. Then using the laws of matrix exponentials, we derive an ODE for the correction terms
\begin{equation}
\frac{d}{dt}\begin{bmatrix}y_{1}(t)\\
y_{2}(t)
\end{bmatrix}+\begin{bmatrix}\eta/2 & -(\omega-1)\\
(\omega-1) & \eta/2
\end{bmatrix}\begin{bmatrix}y_{1}(t)\\
y_{2}(t)
\end{bmatrix}=0.\tag4
\end{equation}
This latter ODE is non-stiff, and can be solved using any simple integration method. With $y_{1}(t)$ and $y_{2}(t)$ known, $x(t)$ is easily recovered.
To summarize, the principal idea is to start with an excellent initial guess, and to write the true solution as a time-dependent correction multiplied by this initial guess. Solving for the correction is then a far easier problem (read: less stiff) than solving for the solution directly.
The particularly strategy above is known as an “exponential integrator” (more specifically, the Lawson type), and assumes that the nonlinear dynamics can be well approximated by a linear one. For this very specific problem of a damped oscillation, it is also known as a phasor transform.