The pro rata treatment has always been there, back before the Roth conversion income limit was removed, and likely before Roth IRAs even existed in the first place.
One of two things has to be true:
1) Congress removed the Roth conversion income limit to generate more revenue but failed to consider that they would be enabling a "back door" way to make Roth IRA contributions at high incomes, or
2) Congress intended for everyone to be able to contribute to Roth IRAs, but they wanted to make high-income folks submit more paperwork to do so, and high-income folks with existing pre-tax traditional IRA balances and no 401(k) willing to accept a rollover should be excluded for some reason.
Option 1 seems a lot more plausible to me. You're welcome to see it differently.