I’m fairly sure this can be avoided completely because you run your Julia code in a separate operating system process. I haven’t used matlab for a long time, but IIRC the problem here is because matlab likes to set environment variables LD_LIBRARY_PATH (and possibly LD_PRELOAD?) which breaks the invocation of user executables with matlab’s system function (sigh… matlab 
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This problem is described here: Why does Matlab set a custom LD_LIBRARY_PATH when execting "system" on Linux? - MATLAB Answers - MATLAB Central
The solution is to unset the necessary environment variables, or otherwise undo whatever crimes matlab has committed against your OS environment.