The doc in question appears to be looking for a fight over the Iraq issue.
The verdict of the court-martial is a foregone conclusion for a number of reasons but primarily because there is a UN resolution regarding the rebuilding of Iraq and a continued military presence which is permitted by the interim Iraqi government. However, his lawyers will be looking towards the House of Lords and Strasbourg for the real action. I doubt this action will achieve anything - if the doc has a moral objection towards UK foreign and military policy then he should resign his commission - he is two years too late to use the illegal war argument.
However, if there was another war (against a certain neighbouring country beginning with "I" for example) following a similar pattern to the Iraq invasion, then a refusal to obey an illegal order to participate may have a significant chance of success. It is clear from the evidence to Hutton and Butler that the Iraq invasion (no UN resolution, lies over WMD) was emphatically not legal and the leaked advice of the Attorney General blew apart any remaining credibility of the case made for war. In the unlikely event of such military action against Iran, I can forsee quite a few cases of service personnel refusing to participate on the grounds that there is no legal authority for military action and that any such action is in breach of international law, and that orders arising from such operations are likely to be illegal. Back in 2003, no one really thought that HMG would lie over an illegal war but we know better now.