There's a very good reason why most modern kits have seperate door handles.
It sounds like you're making more trouble for yourself than it's worth.
As long as you're not planning on actually opening the doors with those handles, a drop of clear parts cement will do just fine.
If you're really anal about it, you could always drill a very small hole in the back of the door handle, glue in a small pin & then drill a hole in the correct position on the body, insert the pin, position the handle & glue from the inside of the body.
I use this "locater pin" method for parts like antennas & mirrors.