'A malicious rouge of a skipper went to an officer ...'what did the rouge do and what did he receive in return?

The "malicious rogue" attempted to stop Gulliver's progress by complaining he hadn't performed the necessary ritual. In return, the rogue was given twenty strokes on the shoulders with a shoot of bamboo. This would be the same as being given a whipping with a lash.

"Before we took shipping, I was often asked by some of the crew, whether I had performed the ceremony above mentioned? I evaded the question by general answers; "that I had satisfied the Emperor and court in all particulars." However, a malicious rogue of a skipper went to an officer, and pointing to me, told him, "I had not yet trampled on the crucifix;" but the other, who had received instructions to let me pass, gave the rascal twenty strokes on the shoulders with a bamboo; after which I was no more troubled with such questions."