As I understand it.
You can release source code under the GPL and people can modify and redistribute that source code under the GPL and use it to build binaries for their own use.
However if your users distribute binaries they will likely be in violation. To distribute binaries built from GPL code users must also provide the "corresponding source code", which the GPLv3 defines as.
The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.
I'm no lawyer but I don't think Mathematica fits any of the exceptions and clearly wolfram won't allow distribution of Mathematica's source code under the GPL. So I would consider binaries built with Mathematica from GPL code to be un-distributable.