Powershell Interaction with Excel (Highlighting Cells)
While this isn't a direct way to speed up PowerShell interaction with Excel, I suspect most people having this problem will find this helpful.  I ended up writing a VBA macro ("Sides") that opens in a third workbook, along with the two of interest.  I then call it from Powershell.  All together, I came up with: 

$excel= New-Object -ComObject "excel.application"
$excel.Visible=$true
$ocomp1=$excel.Workbooks.Open($WorkingDirectory+"Discrepancies1.csv")
$ocomp2=$excel.Workbooks.Open($WorkingDirectory+"Discrepancies2.csv")
$macro=$excel.Workbooks.open("\\dshfs03.dgoz.dccz.ccnz\psst\Aram\Highlighter.xlsm")
$excel.run("Sides")


This runs really smoothly and does exactly what I want.  Granted, you have to know a little VBA, but that wasn't a problem for me.