Disentangling the two is fine, which is what everyone does. Obviously, Anthony Rizzo is really good and he's being paid little money. That's very intuitive.
The difference, as an economist would like to say, is at the margins. Bryce Harper in has last two years as a free agent is going to provide, by $/WAR's standard, something like $60-80 in surplus value. Are five years of Chris Archer (whose worth somewhere around $80-100 in surplus value) worth two years of Bryce Harper plus a prospect? No.
I understand the limitations of that analysis. I do understand teams do have some form of $/WAR that likely adjusts for market, position, offense/defense, etc., so this is more of a critique of using linear $/WAR. IMO, it's one of those things that's not very useful unless it's done correctly.