It is possible to increase natural regeneration, find equipment that gives regeneration (with necklace of rapid healing of cause!), additionally you can be candle-born trollish healer (but this is not requirement) and have healing skill at 100.

You can just laugh using whip, reading messages "You feel some remorse. You feel as if behaving in proper form.", and just waiting till alignment moves towards L.

I don't know whip mechanics very well, but I suggest:
1) Damage taken should be based on the whip, (don't know weather it works this way now). If you use Whip of the snake and has good whip skill - damage should be higher.
2) While self-flagellation PC's perception shouldn't work (for now I noticed that PC doesn't receive great strength waning messages.).
3) Self-flagellation could reduce permanently: max HP, Ap, natural HP regeneration, and maybe St, Dx, To, Pe & Speed if it moves alignment toward L.
4) Alignment shouldn't be increased after it reached L- (don't know weather it works this way now). If you are already lawful for what you should whip yourself?
5) If PC has some equipment that give regeneration, game should tell: "Maybe you should get rid of some protection".
Natural regeneration and healing skill shouldn't work some time after self-flagellation.
6) Add chance to critically hit yourself with whip (more alignment, but risk of bleeding, stunning, massive damage or even death).

If some of those will be implemented PC will really suffer from self-flagellation as it should be...

Maybe this should be a separate issue... Why sacrificing gold could change your alignment without limit but giving gold to beggars has a limit?..