Thompson, the former Channel 4 Chief Executive, attacked the BBC’s critics at a lecture to the FT New Media and Broadcasting Conference in London on Monday night. He claimed that the BBC had the position of having to stand up for the "widest range of ideas".
The televised showing of Jerry Springer - The Opera on BBC2 attracted a record 50,000 complaints from viewers after it depicted the "Jesus-character" as singing that he "feels a little bit gay" among many other controversial incidents.
However, Thompson said, "Our duty is not to be swayed by short-run moral panics or claims about this trend or that trend but rather to consider the issues around broadcast as objectively and dispassionately as we can."
Thompson added, "I do think the organisers of some of the protests, in particular Christian Voice, should reflect carefully on what happened," said Mr Thompson. "Actions have consequences and even if you yourself do not intend to intimidate or threaten, publishing private phone numbers and addresses on the web may lead someone else to do just that.
"The volume of protests was something we did take into consideration, because it showed the widespread strength of feeling. But even if around 50,000 different people really had registered their disquiet, that number has to be considered alongside the 1.8 million who eventually chose to watch Jerry Springer and indeed the 25m households we serve altogether."
With regards to many email protests against the showing, Mr Thompson said, "Small pressure groups can use the internet, e-mails and other modern communications tools to give a false impression of size and weight."
The Times newspaper reported that Stephen Green, national director of Christian Voice, responded to Thompson’s speech by saying, "This is not an issue of freedom of speech, but a case of broadcasting people not knowing the civilised limits and having to be told them."
A glimmer of hope was seen for protesting Christian groups however, as Mr Thompson, a practicing Christian himself, admitted that the BBC had "plenty more to do to reflect religion positively." He added that there was that had to be done to connect the broadcaster to the Christian population in the UK, which according to the last national census, stands at over 70%.
Thompson said, "In my view we have plenty more to do to reflect religion positively on our airwaves particularly Christianity where, despite some real advances in recent years, there is still something of a creative deficit."