How to solve the violations of the Law of Demeter?

A colleague and I designed a system for our customer, and in our opinion we created a nice clean design. But I'm having problems with some coupling we've introduced. I could try to create an example design which includes the same problems as our design, but if you forgive me I'll create an extract of our design to support the question.

We're developing a system for the registration of certain treatments for a patients. To avoid having a broken link to image I'll describe the conceptual UML class diagram as a c# style class definition.

class Discipline {}
class ProtocolKind 
{ 
   Discipline; 
}
class Protocol
{
   ProtocolKind;
   ProtocolMedication; //1..*
}
class ProtocolMedication
{
   Medicine;
}
class Medicine
{
   AdministrationRoute;
}
class AdministrationRoute {}

I'll try to explain a bit about the design, a protocol is the template for a new treatment. And a protocol is of a certain Kind and has medications which need to be administered. Per protocol the dosage can differ for the same medicine (amongst other things), so that's stored in the ProtocolMedication class. AdministrationRoute is the way the medicine is administered and iscreated/updated separately from the protocol management.

I've found the following places which we'll have a violation of the Law of Demeter:

Violations of the Law of Demeter

Inside of the BLL

For example, inside the business logic of the ProtocolMedication there are rules which depend on the AdministrationRoute.Soluble property of the medicine. The code would become

if (!Medicine.AdministrationRoute.Soluble)
{
   //validate constrains on fields
}

Inside the repositories

A method which would list all the protocols in a certain Discipline would be written as:

public IQueryable<Protocol> ListQueryable(Discipline discipline)
{
    return ListQueryable().Where(p => (p.Kind.Discipline.Id =