Just because there are only two possible outcomes doesn't mean that they are equiprobable. Not all coin tosses use a "fair" coin.
The percentages the comment you're responding to provides aren't probabilities, but damage fractions; 50% isn't a 50/50 likelihood, but 50% damage of the 100% case.
Fair coin flips have 50/50 odds. If we say that you get $100 if it comes up heads, and $0 if it comes up tails, then the expectation value for the money you'd have afterwards is $50=0.5*$100 + 0.5*$0. If it was an unfair coin with 30% odds of coming up heads, then your expectation value is $30= 0.3*$100 + 0.7*$0. And so on. The fact that the outcomes are dollars or damage percentages is irrelevant to the calculation.
* Successful cover up (0% damage).
* Failed cover up (100% damage).
* Don't bother (100% damage).
So if doing nothing and failing to cover up lead to the same result, you might as well give a shot at successfully covering up. Whatcha got to lose?
It is assumed not bothering is 100% damage because the screw up is apparently bad enough to warrant attempting a cover up.
In terms of risk analysis, rationally considering a coverup is in the same ballpark as rationally considering shorting a stock, in the sense that making the wrong call can cost a whole bunch more.