The graves wouldn't have come from St John's Church during the digging of the foundations for St George's Hall.
St George's Hall was built on the site of the original Infirmary.
St John's Church was much further back as this map of 1836 shows.
The graveyard of St John's became St John's Gardens.
It's also unlikely that they were graves moved from other churches.
Municipal Cemeteries were created simply because graveyards in churches became full and were then closed for further burials.