Thanks BD. That looks like a good alternative for short PDF's, I am looking for a scriptable capability so I don't have to drag and drop pages in the correct order. I came across a demo version of PDFpen, a fairly well AppleScript-able app, and their tech support e-mailed me an Apple Script which was basically equivalent to the shuffle pages option of the Automator workflow action. I was able to edit their Apple Script to reverse the pages of the even page PDF and it assembles the two PDF scanned files in the correct order. It just requires some manual work to open the file in the PDFpen app, then run the Apple Script, then select the even page PDF. I am still trying to get a more turn-key package wrapped around this so it's easy enough that a Caveman can do it.
http://www.smileonmymac.com/pdfpen
P.S. - Now some of the latest multi-function duplex printers have duplex sheet-feed scanner capability so this wouldn't be a common issue for those with the newer units, but some of the older models, I just got an older refurbished Brother MFC-8660DN from Staples.com since it has OS 9 and OS X drivers, and it can only scan one-sided even though it can duplex print, the new models only have OS X drivers.