Beaghmore is definitely not alone.
There are many sites throughout Europe that are built over previously cultivated land.
One example is an interesting sequence at Machrie Moor, where two adjacent timber circles where replaced by a pair of stone circles but there were at least two episodes of cultivation between the structural phases suggesting a significant break between the abandonment of the timber phase and the construction of the stone monument.
I know I bang on about Bradley rather a lot but I can recommend his 2002 book "The Past in Prehistoric Societies" to anyone who is interested in how our ancestors may have viewed their past.