If you wanted to kill HFT, it's actually pretty easy. Just make the minimum increment incredibly small. In other words, let people trade at $.0000000001 increments. No fees needed.
The idea you suggest already exits for stocks in the US with very high prices because the minimum increment doesn't scale with stock price. For example, Google is $700 a share, making the minimum $0.01 price tick equivalent to 0.0014% vs. 0.08% for a $15 stock like Bank of America. HFTs generally don't even bother with stocks like Google because they aren't profitable enough. The rebate and value of making a tick goes down as price increases. This causes spreads to widen and these stocks are generally harder to trade for the buy-side. Not a good situation.