As for the thoughts that we should have wrapped him up before the season, I personally was still worried about the course he was on, and if the 2013 playoffs or 2012 season was a better indicator of who he would be, and I think the extra dollars we are paying if we end up signing him are actually a reasonable tradeoff for both Cespedes (and his trade value) and increased certainty through a full 2014 season of him demonstrating health, focus, and competence.
An interesting thought - that some of what we might wind up paying prospectively is in effect the premium on an insurance policy the RS had in place to confirm his 2014 value, rather than plunging in blindly in early 2014 on the unproven belief that he'd be worth an elevated salary. To take the analogy further (maybe too far), a lot of us complain about paying the premium on our own coverage when it comes due because we never had a claim against the coverage. The value of coverage on a risk that didn't materialize seems too intangible, but it was substantial because it allowed us to hedge against the risk.
Looked at that way, if his 2014 salary in retrospect was below market, some part of a prospective "over-payment" simply pays the 'premium' for 2014 'insurance' and amortizes the catch-up payment for 2014's below market salary..
(Of course, I'm too lazy to confirm that his 2014 salary was below market.)