Here is some advice for you: Never, ever, change any original BtS file. If you are modifying things, make a mod. This is what they are for. You may have just learned the usefulness of this advice the hard way if you have been changing BtS instead of making a mod.
On the other hand, just deleting a religion should not bother the Python. You should turn on Python exception reporting and the various logging options so that you can see what is actually going wrong. These are controlled via the CivilizationIV.ini file. In that file set HidePythonExceptions to 0 and LoggingEnabled to 1. You should end up with various files created in the BtS Logs folder any time you run the game. Any Python error should cause a pop-up that explains what the problem is, and the PythonErr.log file should hold a copy of the same information. That information is what you need to determine what the problem is.
It is also possible that Confucianism is mentioned in one or more XML files that are not in BtS. Some files from Warlords are loaded, as are some from vanilla. The only files in BtS are the ones that were changed or that are new (much like when you make a mod, you only need copies of the files that you are changing in the mod). I don't know of any that would mention religions, but that doesn't mean there aren't any.
I also have to wonder what you did about the CIV4CityLSystem.xml file since it mentions the 4 Confucian buildings and if you make a mistake in that file bad things could happen. So when you say "removed every instance of confucianism in the xml" the question is, are you sure? If you only removed it from the religion info and building info files then you missed some, including (but possibly not limited to) CIV4CityLSystem, CvCivilizationInfos, and CvUnitInfos. On the other hand, you can ignore any reference in any file in XML\Text (the will keep using a little memory, but otherwise do nothing).
But I don't think any of that is likely to have an effect on the Python from BtS. It may, however, have an effect on some Python that was added or changed for your other modifications.
Oh, and by the way: there are not 6 religions there are 7. Removing one would leave 6.