I can certainly see it being the wrong call in the end. I honestly don't feel comfortable assessing how the PS4 version will do or whether or not the money was worth it. I think a lot of it is going to have to do with questions like:
1.) Will it release full price?
2.) Will it have compelling "Game of the Year" or "Complete Edition" content?
3.) How well reviewed will it be?
If it's a year late $60 port of the game as it existed on the Xbox One a year previous with little to no technical improvement from the added PS4 horsepower, and was an ~80 score on Metacritic anyway, then yeah this thing is going to be a disaster. But let's say it's $40, or there's noticeable upgrades and has significant new (even if not exclusive) content, and it's a critical darling? If you didn't already buy the Xbox One or PC version in the interim (in which case Square Enix already got your money and nothing was lost for them), I think this could still be a successful title next year. I don't expect it to compete with whatever the 2016 holiday lineup is, but I think it could be above "BOMBA" territory.
But yes, I could easily see this backfiring for them and hurting PS4 sales to such a degree that the MS deal no longer makes sense.