MuPDF is GPL-ed, yes.
Using GPL-ed thirdparty components in your software doesn't prohibit its commercial usage (it just requires you release the source code of your software). So... your problem isn't the GPL per se, it's that you aren't willing to release your source code, right?
But... Artifex (the company behind MuPDF, Ghostscript, GhostXPS and GhostPCL) is willing to give you a license for MuPDF (as well as for its other products) for commercial use, which then doesn't require source code publishing of your stuff.
