Nils, Marcin
Problem is even worse. 32-bit Python is not compiled LargeAddressAware, meaning it will only be able to address 2GB of user addressable memory space per process thread running on either 32-bit or 64-bit Windows.
If working outside ArcGIS Desktop on 64-bit OS, use a 64-bit Python as an alternative environment for OSGeo processing--the GDAL libraries and NumPy in this case. You'd need to keep 32-python as primary for correct ArcGIS ArcPy functions.
If just a little more head room is needed to run 32-bit Python code to completion, it is possible to set 32-bit Python executables LargeAddressAware, so modified it can use a 3.2 GB in 32-bit OS, or a full 4GB of user addressable memory space in each thread in 64-bit OS. Several forum threads with details.
Stuart