Can I ask why you're rewriting code on your production server on the fly without the aid of the rest of your tool chain?
In any good development shop you make a change, your CI server picks it up, builds it, and creates a release candidate you deploy. Every change should be checked into source control and built by your automated build bot.
At that point the difference between changing an annotation and an XML configuration file should be moot. I'd think the annotation would be easier because you can still mess up the syntax of the XML file pretty easy (e.g. "Can you change the blahblah label to System & such?" That ampersand will hose your system when you get it to production).
Well, there's always some genuine configuration that contains the actual differences between environments, like DB connection and API keys, and which isn't going to be part of the automated build.
But that's a tiny subset of what architecture astronauts try to label "configuration".
In any good development shop you make a change, your CI server picks it up, builds it, and creates a release candidate you deploy. Every change should be checked into source control and built by your automated build bot.
At that point the difference between changing an annotation and an XML configuration file should be moot. I'd think the annotation would be easier because you can still mess up the syntax of the XML file pretty easy (e.g. "Can you change the blahblah label to System & such?" That ampersand will hose your system when you get it to production).