So now we know...

thought they had that mind reading device and the "prisoner" (don't want to be a spoiler so I won't name names) so they shoulda been able to get enough english outta that guys mind to be able to write that message

Agreed on the shuttle. I can't think of a reason the aliens keep at a distance though, instead of just killing everyone on board and take the ship themselves. They don't really look like they need the technology, and they seem to be more interested in human fysiology than outdated ancient tech.

according to pre-series-plot, aliens are interested in the huge energy-capacity of the Destiny.The closer to "the center of the universe" you get, the less usably energy there is, that's why the aliens want destiny to "harvest" it's energy. I think they didn't pursue their attack, because they know quite well that they have to wait for a special moment, because they don't stand a chance in direct fight without wasting energy. I do agree on the shuttle and the prisoner-theories of yours though.

It's more reasonable to assume that they gleaned what English they knew from the English-speaking human whose mind was connected into their neural network. If Rush had enough time to use their network to study the structure of the ship, then the developers of said tech surely could have learned how to say "Surrender." I do like the idea of energy-conservationists though.