Is there a way for a value from a config file to contain empty lines?

\n is the escape code for a newline. Try using those instead.

The get interface provides substitutions that can be used for a suboptimal work around to the parser's strict handling of new lines:

> cat test.cfg 
[test] 
test=one%(nl)stwo%(nl)sthree

> cat test.py 
import ConfigParser
c = ConfigParser.SafeConfigParser()
c.read('test.cfg')
print c.get('test','test', vars={"nl":"\n\n"})

> python test.py 
one

two

three