Thank you Sabian, that did the trick. Here is the command line I used for anyone else having a similar issue:
msiexec /i "\\path to msi" REMOVE=PDFMakerForLotusNotes /qn
I did this on a test machine with a complete Acrobat installed. I ran the above command and it removed the Lotus Notes PDFMaker plugin. I should also note that it didn't downgrade my version of Acrobat and all of my custom settings within the application are still there.