Can't really say much about germa here, normally they should be dead or be saved by plot like pound, though BMPs should have already tried to kill them like they did with pound. With pekoms he could just be imprisoned, he has tamago's friendship so could survive as a prisoner.
Germa are tricky, we don't really want them in story, they have ways to create plot holes too if just kept alive. Of course don't see oda killing anyone, doubt any consequence will be added by oda.
Jinbe somehow survived too, and doesn't look like any secret plan with BM.
I wouldn't want to see germa and siblings more in story, I can't see how oda will make use of them without adding convenient plot and holes. Best would be that they were all killed or imprisoned for the rest of the story.