INCOMPLETE.
Certainly you can compute that when $d$ is odd.
For all $d\ge 2$, the surface measure reads
$$
d\sigma_{d-1}(w)=(1-w_1^2)^{\frac{d-3}{2}}dw_1 d\sigma_{d-2}, $$
so our integral reads
\begin{equation*}
\begin{split}
I(a)&=\int_{\mathbb{S}^{d-1}} (1-\cos(a w_1)) \, (1-w_1^2)^{\frac{d-3}{2}}dw_1 d\sigma_{d-2} \\
&=\int_{-1}^1 (1-\cos(aw_1))(1-w_1^2)^\frac{d-3}
{2}\, dw_1 \int_{\mathbb S^{d-2}} d\sigma_{d-2}\\
&=\lvert\mathbb S^{d-2}\rvert \int_{-1}^1 (1-\cos(aw_1))(1-w_1^2)^\frac{d-3}
{2}\, dw_1.
\end{split}
\end{equation*}
When $d$ is odd, the term $\frac{d-3}{2}$ is integer and the right-hand side integral is of the form $\int_{-1}^1 (1-\cos(ax))P(x)\, dx$ for a polynomial $P$, which can be explicitly computed by repeated integration by parts.
For $d=3$ this is very simple, as you do not need any integration by parts. Recalling $\lvert \mathbb S^{d-2}\rvert=\lvert\mathbb S^1\rvert=2\pi$,
$$
I(a)=4\pi\left(1-\frac{\sin a}{a}\right).$$
Proving your conjecture in this $d=3$ case is also immediate, as $\frac{\sin a}{a}$ has a strict global maximum at $a=0$, so $I(a)\ge C_\epsilon >0$ for $\lvert a \rvert \ge \epsilon$.
It may be the case that you can compute $I(a)$ also for even $d$, but that requires some trick to get rid of the square root in $(1-w_1^2)^\frac{d-3}
{2}$.