Yes, it really seems as if the only issue would be message routing and RPC calls being enabled between the BES and the Domino. I'd say that's a solvable issue and I have found a posting in the Technical Knowledge Base at RIM's website (
http://www.blackberry.com/knowledgecenterpublic/livelink.exe/Placing_the_BlackBerry_Enterprise_Server_in_the_same_Lotus_Notes_Named_Network_as_the_mail_server.pdf?func=doc.Fetch&nodeId=18829&docTitle=Placing+the+BlackBerry+Enterprise+Server+in+the+same+Lotus+Notes+Named+Network+as+the+mail+server&vernum=1). It outlines that technically it is possible, just they don't recommend it and they don't support it.
I guess I'll give it a shot...