They would certainly make a decent amount of money if Hurricane Harbor was a separate gate, but at this point it would just be horrible PR. Think of it this way: there are lots of people that already think that the park is overpriced, when you consider the gate admission price, $25 to park in the main lot, ridiculous food prices, locker policy, etc. The free water park is good for word of mouth and helps redeem the park a bit in the eyes of the GP, IMO.
At this point, the water park has been free for five seasons and it has become something people that have visited frequently have taken it for granted. Telling people that they would now have to pay an extra $30 for a water park that has been free for five years would be disastrous, even more so if they didn't add any new attractions to compensate. So while the park could have made a killing had they decided to keep the park a separate gate, as it was originally announced, they decided to make it free, and at this point, changing that policy might bring more money, but I think the damage it would do to the image of Great America would be much more significant.