How can I automatically convert PowerPoint to PDF?

No third party product is needed. As you've noted, PowerPoint can export a presentation as a PDF. With the application of a little scripting, you can achieve your result. I've whipped up the VB Script below. Simply create a file with a name ending in ".vbs", paste the code below.

To use:

 CSCRIPT ppt.vbs "input file name" "output file name"

It's important to note:

• If the name(s) contain spaces, they'll need to be quoted.
• If you don't specify a path for the output file, PowerPoint will put it in your Documents folder.

I've included links inline for references to the various bits.

Option Explicit

Sub WriteLine ( strLine )
    WScript.Stdout.WriteLine strLine
End Sub

' http://msdn.microsoft.com/en-us/library/office/aa432714(v=office.12).aspx
Const msoFalse = 0   ' False.
Const msoTrue = -1   ' True.

' http://msdn.microsoft.com/en-us/library/office/bb265636(v=office.12).aspx
Const ppFixedFormatIntentScreen = 1 ' Intent is to view exported file on screen.
Const ppFixedFormatIntentPrint = 2  ' Intent is to print exported file.

' http://msdn.microsoft.com/en-us/library/office/ff746754.aspx
Const ppFixedFormatTypeXPS = 1  ' XPS format
Const ppFixedFormatTypePDF = 2  ' PDF format

' http://msdn.microsoft.com/en-us/library/office/ff744564.aspx
Const ppPrintHandoutVerticalFirst = 1   ' Slides are ordered vertically, with the first slide in the upper-left corner and the second slide below it.
Const ppPrintHandoutHorizontalFirst = 2 ' Slides are ordered horizontally, with the first slide in the upper-left corner and the second slide to the right of it.

' http://msdn.microsoft.com/en-us/library/office/ff744185.aspx
Const ppPrintOutputSlides = 1               ' Slides
Const ppPrintOutputTwoSlideHandouts = 2     ' Two Slide Handouts
Const ppPrintOutputThreeSlideHandouts = 3   ' Three Slide Handouts
Const ppPrintOutputSixSlideHandouts = 4     ' Six Slide Handouts
Const ppPrintOutputNotesPages = 5           ' Notes Pages
Const ppPrintOutputOutline = 6              ' Outline
Const ppPrintOutputBuildSlides = 7          ' Build Slides
Const ppPrintOutputFourSlideHandouts = 8    ' Four Slide Handouts
Const ppPrintOutputNineSlideHandouts = 9    ' Nine Slide Handouts
Const ppPrintOutputOneSlideHandouts = 10    ' Single Slide Handouts

' http://msdn.microsoft.com/en-us/library/office/ff745585.aspx
Const ppPrintAll = 1            ' Print all slides in the presentation.
Const ppPrintSelection = 2      ' Print a selection of slides.
Const ppPrintCurrent = 3        ' Print the current slide from the presentation.
Const ppPrintSlideRange = 4     ' Print a range of slides.
Const ppPrintNamedSlideShow = 5 ' Print a named slideshow.

' http://msdn.microsoft.com/en-us/library/office/ff744228.aspx
Const ppShowAll = 1             ' Show all.
Const ppShowNamedSlideShow = 3  ' Show named slideshow.
Const ppShowSlideRange = 2      ' Show slide range.

'
' This is the actual script
'

Dim inputFile
Dim outputFile
Dim objPPT
Dim objPresentation
Dim objPrintOptions
Dim objFso

If WScript.Arguments.Count <> 2 Then
    WriteLine "You need to specify input and output files."
    WScript.Quit
End If

inputFile = WScript.Arguments(0)
outputFile = WScript.Arguments(1)

Set objFso = CreateObject("Scripting.FileSystemObject")

If Not objFso.FileExists( inputFile ) Then
    WriteLine "Unable to find your input file " & inputFile
    WScript.Quit
End If

If objFso.FileExists( outputFile ) Then
    WriteLine "Your output file (' & outputFile & ') already exists!"
    WScript.Quit
End If

WriteLine "Input File:  " & inputFile
WriteLine "Output File: " & outputFile

Set objPPT = CreateObject( "PowerPoint.Application" )

objPPT.Visible = True
objPPT.Presentations.Open inputFile

Set objPresentation = objPPT.ActivePresentation
Set objPrintOptions = objPresentation.PrintOptions

objPrintOptions.Ranges.Add 1,objPresentation.Slides.Count
objPrintOptions.RangeType = ppShowAll

' Reference for this at http://msdn.microsoft.com/en-us/library/office/ff746080.aspx
objPresentation.ExportAsFixedFormat outputFile, ppFixedFormatTypePDF, ppFixedFormatIntentScreen, msoTrue, ppPrintHandoutHorizontalFirst, ppPrintOutputSlides, msoFalse, objPrintOptions.Ranges(1), ppPrintAll, "Slideshow Name", False, False, False, False, False

objPresentation.Close
ObjPPT.Quit

You can print to a PDF printer driver like Adobe Distiller, or any of the many cheaper or even opensource drivers out there.