Our main claim is as follows:
Proposition. Let $(\lambda_n)$ be an increasing sequence of positive real numbers. If $(\lambda_n)$ satisfies
$$\lim_{R\to\infty} \frac{1}{R} \int_{0}^{R} \sum_{n=0}^{\infty} \mathbf{1}_{[\lambda_{2n}, \lambda_{2n+1}]}(x) \, dx = \alpha \tag{1} $$
for some $\alpha \in [0, 1]$, then
$$\lim_{s\to0^+} \sum_{n=0}^{\infty} (-1)^n e^{-\lambda_n s} = \alpha \tag{2} $$
Here, a sequence $(\lambda_n)$ is increasing if $\lambda_n \leq \lambda_{n+1}$ for all $n$. As a corollary of this proposition, we obtain the following easier criterion.
Corollary. Let $(\lambda_n)$ be an increasing sequence of positive real numbers that satisfy
- $\lim_{n\to\infty} \lambda_n = \infty$,
- $\lim_{n\to\infty} \lambda_{n+1}/\lambda_n = 1$,
- $\lambda_{2n} < \lambda_{2n+2}$ hold for all sufficiently large $n$ and
$$ \lim_{n\to\infty} \frac{\lambda_{2n+1} - \lambda_{2n}}{\lambda_{2n+2} - \lambda_{2n}} = \alpha. \tag{3} $$
Then we have $\text{(1)}$. In particular, the conclusion $\text{(2)}$ of the main claim continues to hold.
Here are some examples:
The choice $\lambda_n = \log(n+1)$ satisfies the assumptions with $\alpha = \frac{1}{2}$. In fact, this reduces to the archetypal example $\eta(0) = \frac{1}{2}$.
OP's conjecture is covered by the corollary by choosing $\lambda_n = \log(n!)$ and noting that $\text{(3)}$ holds with $\alpha = \frac{1}{2}$.
If $P$ is a non-constant polynomial such that $\lambda_n = P(n)$ is positive, then $(\lambda_n)$ must be strictly increasing for large $n$, and using the mean value theorem we find that the assumptions are satisfied with $\alpha = \frac{1}{2}$.
Proof of Proposition. Write $F(x) = \int_{0}^{x} \left( \sum_{n=0}^{\infty} \mathbf{1}_{[\lambda_{2n}, \lambda_{2n+1}]}(t) \right) \, dt$ and note that
\begin{align*}
\sum_{n=0}^{\infty} (-1)^n e^{-\lambda_n s}
&= \sum_{n=0}^{\infty} \int_{\lambda_{2n}}^{\lambda_{2n+1}} s e^{-sx} \, dx
= \int_{0}^{\infty} s e^{-sx} \, dF(x) \\
&= \int_{0}^{\infty} s^2 e^{-sx} F(x) \, dx
\stackrel{u=sx}{=} \int_{0}^{\infty} s F(u/s) e^{-u} \, du.
\end{align*}
Since $0 \leq F(x) \leq x$, the integrand of the last integral is dominated by $ue^{-u}$ uniformly in $s > 0$. Also, by the assupmption $\text{(1)}$, we have $s F(u/s) \to \alpha u$ as $s \to 0^+$ for each $u > 0$. Therefore, it follows from the dominated convergence theorem that
$$ \lim_{s\to0^+} \sum_{n=0}^{\infty} (-1)^n e^{-\lambda_n s}
= \int_{0}^{\infty} \alpha u e^{-u} \, du
= \alpha, $$
which completes the proof. $\square$
Proof of Corollary. For each large $R$, pick $N$ such that $\lambda_{2N} \leq R \leq \lambda_{2N+2}$. Then
$$ \frac{1}{R} \int_{0}^{R} \sum_{n=0}^{\infty} \mathbf{1}_{[\lambda_{2n}, \lambda_{2n+1}]}(x) \, dx \leq \frac{\lambda_{2N+2}}{\lambda_{2N}} \cdot \frac{\sum_{n=0}^{N} (\lambda_{2n+1} - \lambda_{2n})}{\sum_{n=0}^{N} (\lambda_{2n+2} - \lambda_{2n})} $$
and this upper bound converges to $\alpha$ as $N\to\infty$ by Stolz–Cesàro theorem. Similar argument applied to the lower bound
$$ \frac{1}{R} \int_{0}^{R} \sum_{n=0}^{\infty} \mathbf{1}_{[\lambda_{2n}, \lambda_{2n+1}]}(x) \, dx \geq \frac{\lambda_{2N}}{\lambda_{2N+2}} \cdot \frac{\sum_{n=0}^{N-1} (\lambda_{2n+1} - \lambda_{2n})}{\sum_{n=0}^{N-1} (\lambda_{2n+2} - \lambda_{2n})} $$
proves the desired claim together with the squeezing theorem. $\square$