Steve,
While this wouldn't be an experiment (the patient factors in the charts are an observation you make, not something you design) this is a perfectly reasonable analysis. Just like folks run regression models on cross-sectional data all the time that isn't experimentally designed, so too you can run logit models on data from a chart audit. In fact, my first experience with what's not called an unconditional logit model was with just such data - case file data from a state prison system that I used to predict some particular inmate choices.