Here are a few comments:
1) I like the example of a cylinder, slightly more complicated than $S^n$. This satisfies the constancy in the problem. It is symmetric in having a transitive group of isometries, but the group of isometries is not doubly transitive.
2) We can solve the problem if for any points $p$ and $q$, we can exhibit an isometry $f$ taking $p$ to $q$. And there is an obvious candidate for such an isometry: Choose a geodesic $\gamma$ from $p$ to $q$. Then parallel transport along $\gamma$ takes the tangent vectors at $p$ to tangent vectors at $q$, and takes small geodesics starting at $p$ to small geodesics starting at $q$. This creates a map $f:B(p,r)\rightarrow B(q,r)$, where $r$ is the minimum of the radii of injectivity at $p$ and $q$. We need to prove first that $f$ is an isometry on its domain, and then that $f$ can be extended to the whole space.
3) To prove that $f$ is an isometry, it suffices to show that the minimal ball $S$ containing $p_1$ and $p_2$ has the same volume as the minimal ball containing $f(p_1)$ and $f(p_2)$. Then, by David Speyer's reformulation of the hypothesis, the two balls have the same radii, and the same diameters, and the same distance from $p_1$ to $p_2$ as from $f(p_1)$ to $f(p_2)$. This may be useful because if $S$ has (e.g.) twice the volume of $f(S)$, then we can identify a decreasing sequence of balls $S_i$ where $S_i$ has twice the volume of $f(S_i)$, so we can identify a particular point where the isometry fails.