I don't understand what you mean by the margin of error being different on Lv0 mobs vs merit party mobs.
The amount of relic procs in the group of melee hits should be equal to the amount of relic procs in the group of critical hits. The distribution should be equal between both groups. (If not, then of course this method is faulty.)
Assuming the distribution is equal, then just knowing the number of critical hits, and the number of procs in that pool should be sufficient. (Which is easy to record using KParser.)
The crit rate compared to the regular hits shouldn't affect anything. An analogous situation would be parsing hits for 2hours, but only choosing the sample size of the last 30 minutes of parsing. The distribution in the first 1.5 hrs = distribution in the last .5 hours. This works for any time x. Assume a parse for y hours, the distribution of hits after the first x minutes of parsing is equal to the distribution of the remaining y-x minutes. The ratio of y

plays no role in determining the rate of proc.