In Chapter 3 of Chris Schommer-Pries's PhD thesisChris Schommer-Pries's PhD thesis, surfaces with corners (more generally, manifolds with faces) are equipped with extra structure called a "halation", with precisely the goal of making the gluing operation a pushout. The topic of making the gluing operation into a pushout in the smooth category is discussed (and motivated) in some detail, quite lucidly.
Added: Alternatively, you could work in the microlinear category, where the problems we are discussing do not arise, and the naive gluing operation is a pushout. See e.g Basic Concepts of Synthetic Differential Geometry by Rene Lavendhomme.
Added 2: References for the "just add collars" approach are:
- T. Kerler and V. Lyubashenko, Non-Semisimple Topological Quantum Field Theories for 3-Manifolds with Corners, Lecture Notes in Math. 1765, Springer-Verlag, Berlin (2001).
- J. Morton, Extended TQFT's and Quantum GravityExtended TQFT's and Quantum Gravity, Ph.D Thesis (University of California, Riverside).