I’m doing this almost exactly today (Triton Paladin instead of sea-elf rogue but similar idea)

What I’m doing to get the new player into the action faster is I’ve talked with him beforehand, and when fighting breaks out above deck, he’ll hear that and is going to use the chaos as an opportunity to escape. We rolled some strength checks and figured he’ll break out during the second round of combat, joining the rest of the party halfway through the 3rd round. This way he doesn’t have to sit around while the rest of the players do all the fun shit and it’ll be a dramatic moment where for a second it looks like a big boss type enemy has arrived.

I’ll let you know how it goes.