More specifically - do you have ONLY penny stocks in that account, or do you have some higher price stocks there too?
If the latter, you are not buying penny stocks on margin, you are simply buying them in a margin account. In actuality, you are borrowing against the truly marginable stocks you hold and using the borrowed money to buy a penny stock.
This is common. I do it all the time in my Schwab account. Not sure if this is your situation but it is far more likely than ETrade allowing you to buy a penny stock on margin.