There actually is a major controversy whether we can be mechalel Shabbos for metzitzah nowadays. We aren’t mechalel Shabbos to heat up the water for the baby because even though the Gemara says we should, the sakanah no longer exists. There are poskim who say that since according to the Gemara metzitzah is also for a sakanah that we no longer believe exists then one is not allowed to be mechalel Shabbos for it.
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