An astute commentator noted that I never posted an answer to R' Akiva Eiger's question. I'll preface the answer with another question that led my son down the right track. The rule by monetary law is ain holchin b'mamon achar harov. Why should any father give pidyon haben money to a kohen to redeem his son? Whether or not the kohen gets his $5 is a monetary question, and since paternity is determined only by the assumption that rov be'ilos achar haba'al, there does not exist sufficient proof to warrant the father having to pay anything!
The answer is that the issue of paternity is a completely independent from the issue of whether or not the kohein must be paid. First we use rov to determine paternity; once the issue of paternity has been resolved, an offshoot of that determination is that the person we label the father is now obligated to pay for pidyon.
The same approach can be used to resolve R' Akiva Eiger's question. Where a person who is chayav sereifah gets mixed up in a group of people all of whom are chayav sekilah, we cannot use rov to directly address the question of what form of misa to administer. However, we can use rov to first determine paternity; once the issue of paternity is resolved, it follows that killing the person who was labelled "father" through rov may deserve a more stringent form of punishment.