Goddammit, I hate working with Architect Astronauts. I feel your pain brother. Do they actually have a actual, functional reason for doing so other than "it's a standards"? Is this decision going to lock them into a specific EE container vendor (say WebSphere)? That is so 2002; very few people have a real need for it; and in fact, SOAP has been pretty much ignored by most practical, successful implementations. Unless they have a real need for more reliability than what it is provided by JMS or SOAP-over-HTTP alone, you are in for a trip.
Check the Apache CFX site for some examples (specific to CFX).
http://cxf.apache.org/docs/soap-over-jms-10-support.html
The rule of thumb would be to really use the bare minimums, and not the full stack. If your architect astronauts still insist in using the whole thing, you might just be walking into a world of pain. Sorry.
EDIT:
BTW, what application container will you be using? WebLogic, JBoss, WebSphere? And which web service framework? Apache CFX, Axis?
Architects astronauts will love to say that those are implementation details. Bull. Any decision on a system whose change carriers a great cost (or whose implementation carries significant savings) is an architectural decision. These pretty much dictate how things will be implemented (and what the cost of change will be) so determining early on which you will be using is an architectural decision except with very self-contained systems.
A few more links on this controversial subject:
http://www.subbu.org/blog/2005/03/soap-over-jms
http://parand.com/say/index.php/2005/03/29/soap-over-jms-no-such-thing/