The Foreign Office - what side is it on?

In her now dated but still hilarious book Members Only, recounting her adventures as a journo inside Westminster, Frances Edmonds relays the tale of a visitor asking for directions to the Foreign Office:

"Which side is the Foreign Office on?" he asks a passing police officer.
"Well," says the officer after some thought, "they're supposed to be on our side. But sometimes I wonder."

Sure enough, the account of Foreign Secretary William Hague losing his temper in discussion with senior Tory MPs confirms that this perception is still extant:

He [Hague] lost his rag when outspoken Tory Douglas Carswell told him he was 'under the thumb of pro-Arabist' diplomats in the Foreign Office.
'The Foreign Office displays a kind of bigotry towards Israel,' said Mr Carswell. 'The whole idea of self-determination in the Middle East is anathema to some Foreign Office people. It is anti-Israel just as it is pro-EU.'.

He wasn't the only one either:

Robert Halfon told Mr Hague: 'The Foreign Office has not done enough to stop the delegitimisation of Israel. We must speak up for its right to exist.'
Right-winger Priti Patel said: 'We must be more critical of the Palestinians for not giving up violence.' And Nick Boles, a close ally of David Cameron, claimed that the Foreign Office had not done enough to condemn the Palestinian National Authority for glorifying suicide bombers.

Hague himself strongly denied this:

Mr Hague was furious at Mr Carswell's personal onslaught. 'You are living in a fantasy world and talking total nonsense,' he told him. 'The Foreign Office is not pro- Palestinian. I have never heard such claptrap.'

One has to wonder, though, if there's no smoke without fire. There certainly seems to be recurring clouds of anti-Israel smoke from the FO - the Yes, Prime Minister episode A Victory for Democracy features the FO ignoring a Prime Ministerial request to abstain from a UN resolution condemning Israel. Seems like very little has changed in public perception.