The flash lifetime specifications seem to be very conservative, and based on programming and operation at worst case temperature extremes.
Most of the current production HCS-12 parts are specified at 100 erase write cycles.
In practice, some people have reported several thousand erase write cycles on HCS-12 parts at room temperature with no signs of problems.
Some of the early MC9S12D series parts had errata associated with flash, so check the errata for your mask set.
As long as you don't erase flash automatically at frequent intervals, and you're not operating at the ends of the temperature range, you shouldn't have to worry.