Doesn't a discount align the incentives better? Is there active resistance to discounts in the investor community? Among angels at least, I personally haven't seen it...
The only real way to keep the early investors and founders exactly on the same page with regards to increases in valuation is to have the early investors convert as early as possible, or in other words, an ordinary equity / Series A style round. But this is something early founders are trying to avoid because of the uncertainty of the company value, the cost of the legal work, and requirements involved once you have third party investors.