So, probably not a 50 Shades situation here.
In some places the bodies were double-stacked like history's most disturbing game of Tetris, indicating that while the Greeks may have been great at inventing Democracies and Olympicses, they were shit when it came to digging their holes big enough. Each of the victims died young and healthy, and while the exact cause of death is still to be determined (though it's probably safe to rule out a hug overdose), all signs point to a mass execution.
Well, just the one sign, really.
The best theory as to the identities of the shackled corpses is that they are the remnants of a 632 BC coup against Athens led by Cylon, an "Athenian noble and Olympic champion" and definitely not a cybernetic galactic time traveler. After the coup failed, Cylon hid in a temple and later escaped, but all of his followers were summarily executed. Ancient Greece being a heavily militaristic society, however, the soldiers would have been buried with respect ... right up until those burying them ran short on hole space, apparently.