At 03:00 Tan Yun ordered "Datou, go kill them...", so who exactly did he send Datou to kill? Because later, we saw Tan Yun battle all of the enemies by himself, so that leaves just the people who fled the ship, right?

What I'm trying to say is that the heavily wounded people were left in the dark about the plan and reinforcements for no reason, and they made the only logical choice they could.
They decided that following a maniac who stopped the ship and ordered to fight to the death for absolutely no reason, is not in their best interest and they fled the ship to save their own lives.
Did Tan Yun seriously send Datou to kill these people? I guess we might find out later.

It's all about honor and loyalty. If they value own lives over their sect member safety then they are no good. If they abandoned you now, they will surely abandon you later. He's just secretly removing 'weeds' that would take up precious resources later.(ruthless wuxia MC logic)

...hmmm... so is it a case of "propaganda for the party", a case of underlying Nationalist idea were "weeding out" feeble allies is acceptable?

A sect is only strong because of its disciples and it’s unity. This is why Tan Yun sect is declining, they act on their own while these sects have a united front.

Very valid point that actually echoes with the first episode... So in order to restore the sect, Tan Yun will go full Thanos and wipe out those who don't act for the prosperity of the Sect first. Ok... Twisted, but then again, it does clear the "Curse" cast by the two other Gods in the first ep.

Cold blooded but necessary

Another one bites the dust...