The GPL license is quite clear in how its authors intend it to apply in such a situation: If any part of an application uses or depends on GPL-licensed code, then all parts of that application must be distributed under a GPL-compatible license and the work as a whole is subject to the terms and conditions of the GPL license.
This means that, by having an indirect dependency on GMSH, the closed-source package is violating the GMSH license.
Now, it has not yet been tested in court if the intentions of the authors actually hold up, especially in cases where the final executable is only assembled on the end-user's computer. But do you want to bet your business on finding out?
The second option you presented, of calling an external GPL-licensed executable and depending only on its documented command-line arguments and output is a way to keep your code and the GPL code as completely separate works as far as copyright is concerned. In that case, your code is not considered a derivative work of the GPL code and you are completely free in your license choice.