So then is the only way to take it below 3v to the voltage cutoff? That doesn't sound good for the battery.
Every 10 charges or so, I do exactly that... discharge fully to measure mAH capacity. This lets me know when a cell starts wearing out and not taking as large of a charge as it used to. I keep a log of all my cells, number of charges, and capacity measurements.
I don't think it is necessarily bad for a LiIon cell to occasionally be discharged to its lower limit, cell phones and laptops do it all the time. Might shorten life of the cell a little, but they last so long anyway - and I'd personally rather know if a cell is starting to fail. The only way I know to do this is capacity measurement.
If you want to do capacity measurement to the halfway mark, I don't think that is necessarily bad - just don't think that the result will be an accurate "50%" of full mAH capacity. Again, it's not linear.