Write-ins just don't work under a preferential system, because for a preferential system to work properly, it is necessary for EVERY candidate to be listed. Therefor, everyone needs to include the write-in, which means that they ay as well be on the ballot.
One of the reasons I wrote so many people in was to highlight the stupidity of allowing write ins in a preferential voting system!
I don't see that it is absolutely imperative that all candidates be declared in order for a preferential voting system to be effective. Write-in candidates will be treated just like all other candidates--if they fail to meet a certain threshold, those votes will be realoctated based on second place votes. What's the problem?