In this paper we develop a geometric analysis and a numerical algorithm, based on indirect methods, to solve optimal guidance of endo-atmospheric launch vehicle systems under mixed control-state constraints. Two main difficulties are addressed. First, we tackle the presence of Euler singularities by introducing a representation of the configuration manifold in appropriate local charts. In these local coordinates, not only the problem is free from Euler singularities but also it can be recast as an optimal control problem with only pure control constraints. The second issue concerns the initialization of the shooting method. We introduce a strategy which combines indirect methods with homotopies, thus providing high accuracy. We illustrate the efficiency of our approach by numerical simulations on missile interception problems under challenging scenarios.