I believe the Brits were particularly nasty that day and treated Warren's body so dreadfully is that so many of their officers were killed on Bunker and Breed's Hills. No excuse, mind you, but they never expected the casualties they took that day (but they "won" that battle).
Surely that added to it, but I believe Gen. Warren was well hated by the British already.
The Admiral Warren Inne, so important in the Paoli Massacre, was renamed the General Warren Inne in 1825. As I'm sure you know, "No-Flint" 1st Earl Grey led the Paoli Massacre (which was actually in Malvern). I found it amusing to note that they serve Earl Grey Tea (named after Gen. Grey's son, 2nd Earl Grey) at the General Warren Inne. Perhaps the loyalist bent isn't entirely gone! ;-)
As a side note, I wondered how the men up the hill from the Inne felt about it, as they lay beneath the stone that reads...
Here repose the remains
of fifty three
AMERICAN SOLDIERS
Who were the victims of
cold-blooded cruelty
in the well known
MASSACRE AT PAOLI
while under the command of
Genl. Anthony Wayne
an officer whose military conduct
bravery and humanity
were equally conspicuous throughout
THE REVOLUTIONARY WAR
Sacred
to the memory of
the Patriots
who on this spot
fell a sacrifice to
British barbarity
During the struggle for
AMERICAN INDEPENDENCE,
on the night of
the 20th September 1777
The
Atrocious Massacre
which
this stone commemorates
was perpetrated
by British troops
under the
immediate command of
Major General Grey