As I understand it, the GUI is a wrapper that passes calls to the daemon ergo if you use the cli to make those calls then you should not hurt anything. I am guessing as I did none of the programming. The only pitfall I can forsee is that the gui would not refresh from those cli calls and display previous data but that is a rookie move and I can't imagine this team putting out something that lame.

As usual feel free to correct me guys, I'm just making educated guesses from experience on other projects.