The term "free software" (especially when used as a synonym for free and open source software, FOSS) generally refers to the terms of the software license agreement itself, it does not depend on the flat necessary form for the execution of a program. Otherwise, programs related to a commercial operating system such as Windows or iOS could never be called "free software". Since the GPL is a FOSS license, the answer is clearly yes, a GPL lib is free software, regardless of the platform required to use it.
Regardless of this, note that there is a free MATLAB clone called GNU Octave. If someone intends to write a free library that does not require any "non-free" software, it could make it compatible with GNU Octave under Linux. Nevertheless, to my knowledge, the freedom of a library does not depend on the availability of such a free platform.