In general, I would say yes it's frowned upon, they will definitely ask you why you're applying to both reasons and I'm not sure mentioning your less than ideal GPA will be the best reason in their eyes. It also depends A LOT on the relationship between the two programs. If there is overlap in classes and research already, and faculty in both programs work together already, it may be no big deal and it may seem obvious to them why you would be interested in both. If they generally operate within the same building or department but don't interact and see themselves as distinct programs with different goals and different requirements, then they may look at you as being unclear about your goals. E-mailing current grad students and asking about the relationship between faculty in the two programs might be a good way to find out this info beforehand. Either way, if you think that's what's best for you, you should do it, but be prepared to explain yourself.