The 2012 date has nothing to do with the calendar or numeric system we are using. The Maya, or more likely someone before them, found a significant date in a time we see as being in 3114BC. Note they didn't call it 3114BC (& for that matter, neither did anyone else.
Their Ages are 5125 years long - a strange number considering neither 20 nor 13 will divide into it, indicating, I think, once more that someone else came up with the system, or else there is some over-riding factor that determined the 5125 length.
3144BC + 5125 is effectively -3114 + 5125 which is 2011, but in the calendar there is no year 0 so we add a year. (the supposed year The Christ was born (or the start of the calendar if you prefer) is year 1 not year 0 and the year before is 1BC - no 0 year.
So what we have is the Maya telling us their Age comes to an end on the Winter Solstice of the year 5125 years after 3114BC. Our calendar puts that at 2012 but our calendar is a made up thing, with an artificial start, and, importantly, WAS ADJUSTED
by Pope Gregory (actually by one of his Priests) after the Maya codexes and knowledge was brought back to the Vatican.
I don't believe the Church destroyed all they found; given how they behaved everywhere else, I think they took all they wanted, including people to tell them how to read the codexes and string libraries and then burned what was left. The subjugation of all things Maya after that was enough to make sure the knowledge died.
So I think Gregory found out the date the Maya had for the end of the Age and for his own reasons, adjusted things to make 21/12/2012 the date.