Sam: You need to quantify what you mean by sakanas nefashos.
If everyone was dying, then yes it would be clear sakanas nefashos and we know that bris is not yehareig v’al yaavor.
But the percentage dying are a very small percentage. Do you really think it is higher than the percentage of babies who used to die from bris before they had antiobiotics to treat any infections that came up? And before they knew to sterilize equipment? (Not that I am modeh if it is a higher percentage–I’d still like to know what percentage you require.)