Is it worthwhile even applying? Will my low undergrad GPA kill my chances in getting into this program? How heavily will admissions factor in my graduate school degree/GPA and work experience? Any advice/input will be greatly appreciated.
A lot of this depends on your LSAT score. While your GPA is very low (by law school standards), there are places that will forgive that to a certain degree with a high enough LSAT score. The grad degree/GPA won't help you that much in the law school admissions process, though there are certain schools that will love the work experience; it will, however, be invaluable while applying for jobs in the patent field.
As far as if it's worthwhile, I would say yes. You have a very marketable degree and resume for patent law. Even if you don't attend a top school, you should be able to find pretty solid work as a patent attorney with a Master's in Chemistry and work experience in drug development. While I wouldn't necessarily expect to be on drug patent cases (though your work experience might trump your lack of a PhD), I would be surprised if you couldn't find a patent firm to take you on.