Generally when I mill out 2 layer boards, I ensure in the board design that all throughhole components are connected on the bottom only (apart from resistors and diodes which are easy to solder on both sides). The easiest way to change the design is to put a via hole next to the hole which needs soldering on the top. This via hole can have a piece of wire put through it and soldered on both sides, and the component can be soldered on the bottom.