Yes, the shunning is problematic. But there is one key difference between Jehovah's Witnesses and the Amish, in this respect: The Amish encourage their teenagers to go experience the modern world, before making that commitment. Among Jehovah's Witnesses, that kind of pre-commitment behavior would lead to (reversible) soft-shunning.
I think the rational play for an Amish youth would be to not commit to the religion, but live the lifestyle. That's not really feasible for a young adult who was brought up as a JW child, after a certain age. They would be gradually excluded from their baptized cohorts, even if never shunned outright.
How is shunning problematic. If they didn't shun, they would no longer be amish, or be able to preserve their culture. Perhaps we should appreciate the upside of asceticism.
Note that my comment was about comparisons between the Amish & JW flavors of shunning, rather than the Amish specifically. I believe my first paragraph was clear that I think the Amish model of shunning is the more reasonable of the two.
Let's also notice that you chose to say 'preserve their culture', whereas in the comment you replied to I was speaking of religions (and also, albeit implicitly, cults.) I'll come back to your Culture point, but I have to answer your question in the context of what I meant, not what you meant.
Religious shunning is problematic because it harms the individual. Again using Jehovah's Witnesses as an example: JW children are under intense peer pressure to make their commitment at an early age. They are strongly discouraged from building up a social network outside of the JW domain, or even to pursue higher education. So if a JW child gets baptized at 14, and then when 20+ realizes they are gay (or atheist, or buddhist), coming out as such after making that JW commitment causes them significant social, economic, & psychological harm.
But does it protect the religion? Absolutely. That's the whole point, individual-be-damned (if you'll forgive the pun.)
As to your point about Amish culture: religion & culture can be orthogonal to varying degrees. I suspect the Amish are one of the extreme examples, where religion & culture overlap inextricably. There are many aspects to their culture that are especially precious to them, and so it only makes sense that they wish to preserve it.
But still, it would be willfully myopic to not concede that the shunning harms the individual. Atleast /rumspringa/ gives their youth the ability to make a more informed decision, and even a way to avoid complete ostracism even if they explicitly choose to live as though English, and never make the commitment to be Amish. I give them credit for that accommodation, relative to the shunning that other insular religious groups do.
> religion & culture can be orthogonal to varying degrees
I fundamentally disagree and I think this is where a lot of Westerners get hung up on dealing with other countries. There are non-religious cultural practices for sure, but these are not practiced independent of religion.
I realize it's cool to fetishize them but think of them like the Jehovah's witnesses.