I'd like to think that the regret wouldn't have been instantaneous -- but once the boat set down in the water, I'm sure Nathan definitely felt the discomfort coming from Booth and McKay as the two of them got eerily quiet, probably from the fact that 1) they both just witnessed a murder and 2) they've realized they're stuck in a boat for days with a guy this volatile. And then...there's a chance that Nathan also realized that killing Linde pretty much did nothing to make him feel better -- what if he's still worried that they're not gonna make it to land alive? What if he still feels the pain of losing his brother and that (according to my headcanon) he's still ultimately the one to blame for convincing Samuel to come work with him on the Obra Dinn? Well...I guess his worries would come to an end not too long from then. :')

And I guess any normal guy would be quite timid after seeing gigantic spider demons killing another guy before his eyes! A bunch of the seamen don't reappear in Chapter 6 after they get chased off at the start (':