I believe this commit is causing the issue:
This is what Bill meant with the sentence "We made a change in wildfly that all JAX-RS instances are managed by CDI because of managed beans and such".
So it's WildFly integration code which triggers Weld discovery. I'm not quite sure whether this complies with JAX-RS spec...
Yes, this is a WildFly integration problem. Please file a WildFly JIRA issue.