You know, you're right. At the end of the court martial, Spieksma (the Court) says,

"The Court will not permit you to resign. The Court wishes to add that your punishment is light simply because this Court possesses no jurisdiction to assign greater punishment. The authority which remanded you specified a field court-martial — why it so chose, this Court will not speculate. But had you been remanded for general court-martial, it seems certain that the evidence before this Court would have caused a general court to sentence you to hang by the neck until dead.

And at the beginning, the remanding officer is listed as Captain Ian Frankel. So indeed, the Captain was merciful to the poor bastard yet again by sending him to something less serious than a general court-martial. It was that Court that gave the maximum punishment, not Captain Frankel. He -- along with Sergeant Zim -- tried to go easy the entire time.