I had a somewhat similar problem. I have Python scripts that make this huge feature class of parcels (the parcel feature class has almost 100 fields in its table, if you can believe it). One of the final things my Python script was supposed to do was export this huge parcel feature class as a shapefile. I could manually export it in a few minutes using a geoprocessing tool. I could export it in a few minutes running a model. However, when I tried to export the parcels as a shapefile in the Python script, it just hung up and never exported. I accounted for things like indexes, but Python just choked (no pun intended).
What I had to do was make a VB.NET/ArcObjects console application that would take the feature class and export it as a shapefile. The console application .exe file runs as a "script" and all it does is make the shapefile. This application is based on the "CopyFeatures" example from the ArcGIS developer kit. So there are things in Python that run slowly if at all but will run well as ArcObjects C# or VB.NET.