I think their "price improvers" demanded this of them. However, lets assume it's regulatory cost related or that they've determined that the all in costs of supporting small lot penny stock traders isn't worth it (ie these users generate in commissions less than their all in cost in terms of server resources consumed as well as things like contacting support more frequently). I suspect they do these kinds of demographic analysis to determine which groups of traders cost vs benefit them. Who wouldn't? Possible solutions:
1) Discourage penny stock trading in small lots (which appears to be what they've done)
2) Stop penny stock trading (of course they'd lose all penny stock revenue, including that which is worthwhile -- it's also one less selling point. Even people who don't trade penny stocks might like that they have the ability even if they never use it)
3) Increase commissions on penny stocks across the board
4) Make a more complex commission structure for penny stocks where the bottom tier gets a price increase
If they did 3 or 4, I suspect the impact would exceed just penny stock traders. People considering switching to IB as well as those on the fence / considering leaving, would see a commission price hike that they'd naturally think could be expanded to include their trading (even if they don't trade penny stocks). Because of the negative business impact outside of penny stocks due to the negative perception of a commission hike may be why they decided to go the other route -- discourage the small lot penny stock trading.
All speculation of course.