Perhaps, or perhaps not. I don't think it's entirely clear at present, given the contentious personalities the Germa possess. One thing to keep in mind is that Judge is likely out of action currently. Given that the children are designed to obey his commands, what happens when he isn't there to command them? Do they maintain their most recent orders from Judge, that being to escort the alliance members to safety, or does it open them up to deciding what to do themselves. The latter is the potentially concerning part, given Ichi, Niji and Yonji's lack of compassion that could mean that they wouldn't want to act favourably towards anyone, including the Straw Hats or Sanji.
That all being said, it could also be true that they are aiming to aid the Straw Hats, given that the Big Mom pirates did try to kill them all. Really, I think much of what happens with them will depend on who and where they meet up, if they meet up with the Thousand Sunny then they're likely going to be aiding them, if they meet up with Sanji and Bege then things could go both positively or negatively.