It depends on who you sign, if you get an All Star type player for he cost of a prospect that may or may not make the ML in 3 or 4 years it would most likely be worth it, depending on the amount and length of the contract. Next year Harper is a free agent and you can bet he gets QO, but who ever signs him would gladly give a 2nd pick. The 2nd pick isn't as bad as losing the first pick like last few years.
A player such as J D Martinez can't be offered a QO because he was traded, same goes for Upton.
Qualifying offers will be near $18M this off season, teams will have to be careful who they extend it to because they just might take it. Think Rasmus 2 years ago with Houston.