After all, the upper-stack ebXML CPPA does not seem to have gained much purchase in North America, although it has done better in the Asia-Pacific region and some government circles. In North America, BPEL seems to have much more industry momentum, so once WS-Security (WS-S/T/X/Y/Z whatever) has matured (how long will that be?) will ebMS just fade into irrelevance?
Were I in your shoes, I would ask my customer if they had a compelling reason to go one way or the other. If partnerships or alliances don't dictate the choice for them and you, I'm inclined to back your play and tell you to go ahead with BPEL. It has a lot more supporting infrastructure at this point and (from what I can tell) is the focus for lots more actual implementations and adoptions as well.
If all else fails, cheer yourself up with this statement of fact: Any sufficiently rigorous XML syntax/structure (and both sets of markup qualify) can be transformed into something else equally arbitrary and rigorous using XSLT in the future! Just hope like heck it will be a one-way-only transform!
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