Let $C$ be a strictly convex domain in a $3$-dimensional Riemannian manifold with sectional curvature bounded above by a constant and let $Sigma$ be a constant mean curvature surface with free boundary in $C$. We provide a pinching condition on the length of the traceless second fundamental form on $Sigma$ which guarantees that the surface is homeomorphic to either a disk or an annulus. Furthermore, under the same pinching condition, we prove that if $C$ is a geodesic ball of $3$-dimensional space forms, then $Sigma$ is either a spherical cap or a Delaunay surface.