This makes no sense because he was willing to confront the outsider on the boat where he had access to none of the resources of Demonreach. If he was too weak, then he should have made up some excuse to stash Justine somewhere else. Not confront her on the boat.
I think his thought was "I cannot let Justine set foot on Demonreach." The idea was for the Island to imprison her without taking her there. That's my reading of it, anyway.
As for Thomas, Harry's reasoning is that Thomas's Hunger is turning inward and he is about to turn feral, or die. If Harry brought someone to feed Thomas's Hunger, Thomas would undoubtedly kill that person in his current state. So stasis was the solution to prevent anyone from dying until he can figure out a way to keep Thomas alive.
But for meta reasons, it's to remove some characters and trim things down a bit. Murphy and Thomas out of the picture for a few books will make things leaner and leave more room for new players (or for older characters to take on a bigger role, like Lara). I mean, they're both in most of the books pretty extensively.
Oh, and also it gives Harry something to be sad about that is also a solvable problem.