My mother recently passed away, who was the owner of a successful real
estate company.  She had left the company to me and my brother.  Our
estate attorney had pointed out that you needed to be a broker or at
the very least a agent in order to own your own real estate company. 
The broker, who works for us, tells us that we only have to have a
broker in house for the company to keep running.  She told us that she
got this information from her attorney and from the Indiana real
estate commission.

Currently the business is registered as a LLC, but we where told this
was in error and may not be legit.

My question simply is, in Indiana state law do you have to be a agent
or a broker in order to own a real estate company?  Can me and my
brother keep ownership of the company while our broker runs things for
us?  Please provide some sort of proof if possible.

I dont know what the legalities are in your state, but you could
always go and get your own real estate license - it is not expensive
and you could possibly have it within 1-2 weeks.  Check for
requirements in your state.