I have the same problem with gCal sync. I get calendar notifications, but if I accept them in Google Calendar on the web, or on my phone, they will never go away on Apple iCal on any of my Macs.
This is a straight-up bug.
They need to do two things: 1) Clear notifications from the past. Because, seriously. and 2) Allow user to manually clear all notifications in the inbox, without accepting or declining them.
Otherwise I'm already experiencing these simply piling up with no solution....