2 of 2 when creating a new file, don't affect the old file until the new version is ready

You can't. Either use ed or GNU sed or perl, or do what they do behind the scenes, which is to create a new file for the contents.

ed, portable:

ed foo <<EOF
1,$s/^\([^,]*\),\([^,]*\),\([^,]*\).*/\1,\3/
w
q
EOF

GNU sed:

sed -i -e 's/^\([^,]*\),\([^,]*\),\([^,]*\).*/\1,\3/' foo

Perl:

perl -i -l -F, -pae 'print @F[1,3]' foo

cut, creating a new file (recommended, because if your script is interrupted, you can just run it again):

cut -d , -f 1,3 <foo >foo.new &&
mv -f foo.new foo

cut, replacing the file in place (retains the ownership and permissions of foo, but needs protection against interruptions):

cp -f foo foo.old &&
cut -d , -f 1,3 <foo.old >foo &&
rm foo.old

I recommend using one of the cut-based methods. That way you don't depend on any non-standard tool, you can use the best tool for the job, and you control the behavior on interrupt.