I'm the "GL" who wrote the above-mentioned code for finding what is deprecated, the correct version is at http://lcblog.lernerconsult.com/2014-domain-mapping-wpdbescape-deprecated-fix/
(PHP code did not copy properly into kenzo's post above)
I had to remove the Development version Rev 896459, links on my pages all had the un-mapped domain name.
Checked today for a newer Development version. See https://plugins.trac.wordpress.org/log/wordpress-mu-domain-mapping/ which shows newest now is Rev 940562, 6/29/2014. Quick test of it shows no debug messages, and shows links on my pages with the mapped domain name.