Yes.. for the longest time, this is what i do... arduino ide sent the hex through avrdude.exe inside its installation folder... what i did is made a 'middleman' avrdude.exe just to intercept and display what arguments arduino ide commands the avrdude.exe to do the job and then made my little tool to send the same comand along with *.hex i programmed in avr studio 4 to avrdude and then to arduino board.. i did all this simple trick because i suck at arduino the ide for its slow compile time and the childish workflow... if you want my middleman utilities, just ask, i can attach here.. or else, you may find something else in the net, or you can make one youself in no time. I coded my tools in vb.. ymmv.
Edit: err. If what you want is exactly like you asked, ie from exactly arduino the ide to a non arduino board, then no.. the problem is you dont quite understand the flowchain, as some part i already mentioned, and the bootloader... just use avr studio for that is easier if you dont understand the flowchain yet....
ref: youtube.com/watch?v=LO8nnQZCrMU