PDFPen does what you’re looking for—at least almost.
You can drop a PDF file on to the dock icon and it will open in the app. The app automatically determines whether OCR tracing is needed/possible or not*, and if it is, it asks you to confirm which language(s) you want it to recognise when OCR tracing. The tracing itself seems quite fast—I just tried it on a 15-page text-only file, and it took about 15 or 20 seconds or so.
It won’t automatically overwrite the original file, but simply saving (⌘S) will.
I’ve only used the free trial version (which overlays a watermark on the file, but seems otherwise unrestricted). At $74.95 for the full version, it’s not exactly cheap.
* I don’t know exactly how reliably auto-determining feature is, but it’s worked for me so far. When I open PDFs whose text is already selectable, it doesn’t give me the OCR option; with non-selectable PDFs it does.