Do you mean, for some client you want to use SOAP with attachments, and for others - MTOM? I do not believe you can enable or do this dynamically, because it is part of the service endpoint contract definition.
What we do, we have only one XML atttribute defined as @XmlMimeType("application/zip") and at the same time as @XmlElement(..., required=false). As a result, when this attribute is not null, it is sent using MTOM, and when it is null it is absent from response, and there is no MTOM encoding in this response.
I am concerned if a client can not process mtom encoded attachments, so I like to make mtom optional on the server. (this is an in-house application, so customers will have control over the server) So when server is not mtom-enabled, attachment is send inline.
The javadoc for BindingType annotation states that the annotation may be overriden programmatically. I was thinking maybe I can use that to read mtom configuration from a properties file, but I am not sure how do that.