I've calculated the correct answer to my problem, but don't understand one of the assumptions I made when doing so.
I used the geodesic deviation equation $$\frac{D^{2}\xi^{\mu}}{D\lambda^{2}}+R_{\phantom{\mu}\beta\alpha\gamma}^{\mu}\xi^{\alpha}\frac{dx^{\beta}}{d\lambda}\frac{dx^{\gamma}}{d\lambda}=0$$
to show that on the surface of a unit sphere two particles separated by initial distance $d$, starting from the equator and travelling north (ie on lines of constant $\phi$) will have a separation $s$ after time $t$ equal to $$s=\xi^{\phi}=d\sin\theta=d\cos\left(vt\right).$$ This is similar to Geodesic devation on a two sphere except that question was solved using simple spherical geometry.
The assumption I made was that the second absolute derivative wrt $t$ equals the second ordinary derivative, ie
$$\frac{D^{2}\xi^{\mu}}{dt{}^{2}}=\frac{d^{2}\xi^{\mu}}{dt{}^{2}}.$$ My question is, why am I allowed to make this assumption?
I've been told on another physics forum that the answer is because the problem is framed in terms of Riemann normal coordinate (because the distance the cars travel along their separate geodesics is a linear function of time $t$). I can only assume that in some way this makes the connection coefficients disappear in the absolute derivative equation$$\frac{DV^{\alpha}}{d\lambda}=\frac{dV^{\alpha}}{d\lambda}+V^{\gamma}\Gamma_{\gamma\beta}^{\alpha}\frac{dx^{\beta}}{d\lambda},$$ but I can't see why this is. As I noted in a comment below, I understand it is possible to choose coordinates at a point where the connection coefficients vanish, but I used the ordinary polar coordinates $\phi$ and $\theta$ to calculate the correct answer. To use two different sets of coordinates like this seems like a case of "having your cake and eating it".
The calculation, by the way, is here (my answer to my question): Geodesic deviation on a unit sphere