public class User : Entity
{
    public virtual ICompany Company { get; set; }
}

public interface ICompany
{
    int Id { get; }
}

public class CompanyA : Entity, ICompany { }

public class CompanyB : Entity, ICompany { }

public class UserMap : ClassMap<User>
{
    public UserMap()
    {
        Id(u => u.Id);

        ReferencesAny(u => u.Company)
            .IdentityType<int>()
            .EntityIdentifierColumn("CompanyId")
            .EntityTypeColumn("CompanyType")
            .AddMetaValue<CompanyA>("companyA")
            .AddMetaValue<CompanyB>("companyB");
    }
}
public class CompanyAMap : ClassMap<CompanyA>
{
    public CompanyAMap()
    {
        Id(u => u.Id);
    }
}
public class CompanyBMap : ClassMap<CompanyB>
{
    public CompanyBMap()
    {
        Id(u => u.Id);
    }
}