The crash is probably because your application tries to use Slicer’s ITK, VTK, HDF5, etc. libraries. If you want to use the default system environment, you can retrieve it using slicer.util.startupEnvironment()
.
from subprocess import check_output
check_output(
["/usr/bin/python3", "-c", "print('hola')"],
env=slicer.util.startupEnvironment())
'hola\n'
See details in this post: Subprocess call in Python interpreter results in memory corruption