<p>Context:
  So, I am attempting to build a ridiculously complex domain model.  Talking with the users, there are multiple ways the system will be used (For example: one way is from the perspective of the employee; another way is from the perspective of the employer).  In actuality, they are multiple applications reusing the core domain.</p>

<p>Question:
  Is it wrong to create the domain from multiple perspectives?  For instance, to build the domain as the business is run would mean creating all kinds of relationship classes that carry extra information about the entity and so on...  However, when running from a particular perspective, the picture is much clearer because most of the relationship classes can be rolled into their parent entity.</p>

<p>Ideas? Rebuttals? Am I completely off-base?</p>

I don't think you should try and predefine the 'core domain' up front. Let it emerge over the development process. Additionally, anything that is not common to the 2 (or more) perspectives should not be in the 'core'.
For instance, build a portion of the system from the employeer perspective. This might prompt you to create entities like 'Project', 'Task', and 'Customer'. Then build a portion from the employeer perspective. This might prompt you to build new entities, and to reuse 'Project' and 'Task'. That's when I'd move 'Project' and 'Task' to the 'core library' shared by the rest of the system.
Sometimes you'll find common entities, but related in different ways. In that case the relationship should be injected by the context instead of being built-in with the entities themselves.