As with many formatting nuances in CSV, there is no agreed "standard" for how to handle embedded newline characters in a CSV field.
A common implementation is RFC-4180: Common Format and MIME Type for Comma-Separated Values (CSV) Files, which suggests:
6) Fields containing line breaks (CRLF), double quotes, and commas
should be enclosed in double-quotes.
For example:
"aaa","b CRLF
bb","ccc" CRLF
zzz,yyy,xxx
This is the format that mongoexport
is currently using. If you use a CSV parser compliant with RFC-4180 (eg. SuperCSV as suggested by @evanchooly) it should handle the quoted newlines as expected.
If you need an alternative to the format used by mongoexport
or need more flexibility in your output, you can always write your own export script.