This episode always reminds me of an experience I had in China. I was working with some Chinese scientists and we went into a local town's welding shop to get some custom pieces made. Keep in mind I was in a poor, relatively isolated part of China. I was likely the first, or one of the first, western people the residents had seen in real life. My translator had to run to the bank to pay in cash, and he left me with the 40 year old woman who owned the shop (I was 25 at the time). She took me upstairs to her apartment above the shop. We sat down at her table and just stared at each other in silence, not being able to speak the other's language. At the same time, we burst out laughing. She cracked open a beer and we spent the next 20-30 minutes talking what amounted to gibberish to each other. She or I would point to a random object in the room, and say something in our own language about it.
The Gilgamesh scene puts a smile to my face every time. The alien captain was willing to risk his life, and much more, just for a chance to communicate with another species. It didn't matter if they could understand one another.