Charge a minimum brokerage on every trade and the problems will be go away. Surely not too much to ask to even up the playing field.
For min brokerage, maybe $5 a trade (that's probably a discount of 75% on what most people pay), or if this is too much to bear on penny stocks, maybe on stocks under $1 a share, charge the cost of a single unit of each trade). I reckon single unit trades will quickly dry up and HFT behaviour will have to be modified.