If your wife stays less than 6 month outside of US - Immigration doesn't suspect anything
For the stay 6-12 months outside of US - Immigration can suspect something wrong and suggest filing re-entry, but it's only suggestion. There's no way they can take her Green Card in this case unless she'll say at immigration something wrong proving that she's been permanently staying not in US, but outside of US (for example, she'll respond the reason of stay outside of US that she's working in China).

IMO: Immigration was correct, and your wife was lucky, that she's entered US at SFO, and not at MIA or JFK.