The judge told him: "You have, in the view of this court, sought to make a martyr of yourself and shown a degree of arrogance which is amazing.
"Consequently you have lost any credit you might have been given for guilty pleas."
Dr Kendall-Smith's solicitor, Justin Hugheston-Roberts, told BBC News the doctor was "upset yet resilient" and would be appealing.
"Now, more so than ever, he feels his actions were totally justified and he would not, if placed in the same circumstances, seek to do anything differently."
In a statement read by his solicitor, Dr Kendall-Smith said: "I would wish to thank all those people from all over the world and from all walks of life for their good wishes, their kind thoughts have helped sustain me through the past months.
"I would wish to restate that I have two great loves in life, medicine and the Royal Air Force.
"To take the decision that I did caused me great sadness, but I feel I had no other choice."
Outside court, Stop the War coalition national organiser Chris Nineham called the decision "a travesty of justice".
Dr Kendall-Smith had taken "a very courageous stand" and "paid a very high personal price for the lies of Tony Blair and his government", he said.
An RAF Prosecuting Authority spokesman said: "British troops are operating in Iraq under a United Nations mandate and at the invitation of the Iraqi government."
RAF spokeswoman Wing Commander Ailsa Gough added that the MoD noted the court had upheld the fact that, under the Air Force Act 1955, the orders given "were lawful and, therefore, should have been obeyed".
But CND chairwoman Kate Hudson said military personnel had a responsibility to familiarise themselves with international law on the conduct of war and to act accordingly.
"We all know they cannot hide behind the excuse that they are on the receiving end of orders from on high," she added.
Dr Kendall-Smith, who holds dual British and New Zealand citizenship, had served twice in Iraq before he refused to train for his deployment last year.
He decided the invasion was illegal after studying books and articles.
In mitigation, his lawyer Philip Sapsford described the doctor as "an officer of impeccable character" with an "exemplary record".
"He is a man of great moral courage," Mr Sapsford said.
He was found guilty of refusing to attend equipment fittings and a training course as well as one count of failing to obey an order to attend a deployment briefing.
© BBC MMVI