There is an error of understanding here:
1. Failure to respond to call-out = offence
2. Being AWOL = offence
3. Declaring conscientious objection = NOT an offence
The case appears to have been brought as a result of 2. What should have happened is that it should have been made clear to him that had he returned from leave and subsequently stated his conscientious objection, his case would have been delat with under existing procedures. That doesn't seem to have happened..
And before people go get all high and mighty again, you may be interested to know that at least one officer (a pilot) resigned his commission over Bliar's adventurism in Iraq.