You're making a fundamental error, here.
You can't simply offset those billions of dollars against the number of jobs. You need to look at what would have happened had Ireland not made this deal to begin with. It's fair to say that Apple would never have funneled their profits through the Irish tax haven had this deal not been in place, so the question is really "Are the 6500 jobs, plus however much actual tax revenue was collected, a greater return for Ireland than not having Apple's money in the country at all?"
I don't know the answer to that question, and I won't speculate on the matter, but that's the calculation in play here. Claiming otherwise is either ignorance or bias.