I\'m investigating replacing or supplementing our home grown ORM system with the Entity Framework 4, and I\'m noticing that the latter may end up causing a conflict between
Sure there is. There is T4 template which converts your model to SQL DDL scripts. You can make a copy of this template and put your own logic for name generation into the new copy. After that you just need to set this template in your designer (DDL Generation Template property) and run Generate Database from Model ...
You will find default template in:
%VSINSTALLDIR%\Common7\IDE\Extensions\Microsoft\Entity Framework Tools\DBGen\SSDLToSQL10.tt