Where should a journalist's loyalty lie? It should be an easy answer: with the public. It is something that is preached over and over again. A journalist's responisbility is to inform the public and do what is best for them. That doesn't mean that is what they do though...and what if what is important to the public is not important to whoever runs the newspaper? Do you do what the boss says (after all, it is your job) or do you take a stand by printing (or not) something, quitting, protesting.... what should you do?
Here is what I think. A journalist's obligation is to the public, period. That is why their job exists; to let the public know what is going on in the world. It is up to them to decide what they think of it. Sometimes that means there is controversy over what to do. I think that a journalist should stand up for their right to inform the public...whether the boss agrees or not. Whether or not the reporter wins is not as important to me as knowing they tried to fulfill their responsibility.
Public Relations practitioners are different because they work for a specific company, and their job is to promote that company. So that is where their loyalty lies. Sometimes they may need to make a choice too (for example if a company is being dishonest), but mostly it is clear where their loyalty belongs.
So to summarize simply: Public Relations = company; Journalist= the public