I can't blame Rokurou for falling for that. He's an actual kid, and he doesn't have nearly the amount of context and information we have. The Dark Water's story is pretty believable, especially after seeing Seiichi's memories of the white water planet gaining emotions through contact with him. Combined with using the face of a young girl around his age, begging to save an entire SPECIES, it's a huge responsibility to put on a little kid.
On that note, I just spent the past two days marathoning this manga. This is incredible, one of the most well-written stories I've read in a while. Have yet to find any significant plot holes, everything ties together quite well. This was clearly well planned before the first chapter was even drawn. I sincerely hope this gets an anime adaptation, because while I normally don't bother watching anime this is one I absolutely want to see.