I wouldn't take general chemistry unless 1. you want to go to a school that will only accept that particular chemistry class, or 2. you have biology or chemistry as a back up major.
That being said, if you decide to take another Chemistry class, it will only hurt your chances IF you do not do well the second time around. I personally would focus on my other prerequisites instead, but if you feel that taking another chemistry class would help round out your education a little more, then I would lean towards Chemistry for Allied health.
I've taken both Gen Chem 1&2, and then Chemistry for Allied health at a later date as a "refresher," and that allied health class covered all the topics from Gen Chem 1&2 PLUS some organic chemistry. The good thing was that it focused on topics that actually add to your nursing education - proteins/fats/carbs, pH, partial pressures of gases ect. If you've already taken Anatomy though, chances are that you already have been exposed to all this stuff.
Good luck in whatever you decide to do!