I was a "native", and I'm not so sure this doesn't apply to "natives" as with those who migrated to successfully navigate the social problems of dealing with an intolerant majority or a friend or family member with a particular concern in our affairs. I imagine the problem is amplified for "migrants" of a sort, particularly where their original position was hardened and "xenophobic" as described but it isn't zero for anyone else on this ship either. Lots of social energy is expended on trying to make atheists recant or migrate away on the logic that they should feel bad for "abandoning" other people or their beliefs and that wouldn't it be better to stand with lots of other people. That this is a case for their religion as a social status function might be warranted, but it isn't suddenly a proof for their deity, forms of worship, that other people feel bad because of your lack of subscription to their particular beliefs and systems.
I'm not sure how that warrants the label of "guilt" so much as mutual resentment and animosity that we'd prefer to avoid. Many atheists effectively go underground for this reason to avoid the entire infrastructure where ever possible. I'd say this is a far bigger social problem in the long run than the personal discomforts of families broken apart by faith-related migrations. These individuals bear a measure of social stigma and shame while some others have to deal with divisions in family or social groups. Neither is an acceptable response and individual atheists shouldn't be having to decide which they're more apt to tolerate as a path.