Hmm, I'm shooting from the hip here, but in the <properties> node, when you include a properties file, it looks like you can run jexl expressions/functions in the included file:
e.g.,
etl.properties
current_date = ${date:today('yyyyMMdd')}
etl.xml
<!DOCTYPE etl SYSTEM "
http://scriptella.javaforge.com/dtd/etl.dtd">
<etl>
<properties>
<include href="etl.properties"/>
</properties>
<connection id="log" driver="text"/>
<script connection-id="log">Date: ${current_date}</script>
</etl>
$ scriptella -q
Date: 20130426
So you could do something like the extended jexl functions date, class, text, etc...
http://scriptella.javaforge.com/reference/index.html#Expressions+and+Variables+Substitution for a gpg file, and have your etl.properties have something like
etl.properties
rootpwd = ${gpg:read('rootpwd')}
and maybe it looks for a etl.properties.gpg file that is encrypted, decrypts the file, and grabs the variable out of it and stuffs it into the rootpwd variable so it can be used in the driver's context? That way you're not having to modify your integrations, just update your properties file to support the encrypted data?
We do something similar for our database passwords and such as part of our Puppet/Heira implementation, Heira has a gpg driver that handles the encryption and the rest of the implementation uses the regular heira() function to fetch those variables.