Most bacteria is good bacteria and a good healthy dog is well equiped to deal with bad bacteria.

Freezing won't kill harmful bacteria like Salmonella and E.Coli it will however kill parasites like Neospora which are more of a risk when feeding raw meat and bones.

Raw meat and bones are best fed fresh to a healthy dog as exposure to bacteria etc encourages a healthy immune system. All my dogs get fresh meat and bones as often as possible.

You are perfectly okay to feed raw bones to your puppy. It's up to you which bones you feed.

Glad to hear you're feeding her a steady diet now!