You are right that using a debugger for some game-type development can be problematic. Specifically, as you mention, when the debugger is capturing input and you want your game to capture input, they may be incompatible. Also, when the game is timing sensitve (and we know the game loop is), then debugger can slow down performance enough to matter and/or breakpoints can cause problems.
Hence, being able to debug via print messages is critical. And since doing print message to a screen with a graphical display can be tricky (or impossible), you often need to rely upon the logfile.