The solution is to tell Macports to build universal binaries. This can be done by adding +universal to the command line, for example:

sudo port install jpeg +universal

A more general solution is to add this “variant” to the Macports config. Simply add +universal to the file /opt/local/etc/macports/variants.conf. The file is read-only, even for root, so make sure to force-write the file (:wq! in vi).

And if you want to rebuild everything universal, sledgehammer approach:

sudo port upgrade --force installed