If this is part of the PoS and cannot be changed/has not been yet fixed, I could make it so that PoS does not start automatically, but require an option like -start-pos, or something.
A fix could also be to not split the transaction after calculation, something like:
Verify if the coin is old enough ( 1 Week ? )
then calculates the interest total= coins + interest
then create the new transaction with total and then remove the old coins.
Because the quantity of transaction is not only linked to POS but also POW can generates lot of dust coins, it could be also interesting to have a tool to concatenate coins automatically.
For example POS could be used as a regulator like,
if the coins value > high_limit then split coin
else if coins value < low_limit then if (next coin exist) concatenate coin with the next coin