Difference between the two is - well WMB is a proven okay defender there. They both have power, and both hit for roughly the same batting average. There is a good chance WMB will hit better here than Boegarts would have. But Boegarts would have still been plenty competitive in terms of actually not making outs ... basically a .270/.300 sort of slash line vs a .240/.330 sort of one. I hope the tour in the minors helped Middlebrooks - but pitch recognition is usually born, not made. Guys allergic to walk, very rarely shake that allergy. But there is no reason he can't be a league average 3B. I would have chosen Boegarts, but I get it - and I don't think this is a final verdict on the matter.
Remember, Boegarts can be on the playoff roster - no matter when he comes up (due to the Hanrahan, Bailey, Miller and Kalish injuries). So the pressure to bring him in August was never really there.