The keybinds don't actually reset, but they will always try to accomplish what has been bound to the key each time. Sometimes this means that some powers will not fire off each time and the key will need to be pressed multiple times.
Unfortunately for you, I don't think you can get the granularity you want with the keybinds. Since they are designed to map one or more powers to a key stroke, but without giving the "I win" button, there is no way to allow delays.
I would suggest a number of hardware/software solutions out there that can provide what you want. Logitech provides numerous options as does Razor. I am sure there are many more.
In regards to your anti-spam phaser power, I would suggest you put one fore and one aft phaser power in a single keybind. This way you can press it once and it will take care of your small target.