Hi, I'm new to the creation kit, and I am wondering if there is anyway I can create and esp that will run some commands in the console as soon as the game loads if the esp is active. I was thinking to use it to delete some refID's.

Yes, but it has nothing to do with console commands, you "simply" write a script, which can be simple or impossible for you, depending on how much you know about scripting. Those kind of scripts are usually simpler than others, and could be done by digging through examples that do this (for example the way homes work, when you buy furniture some old stuff is removed, and new stuff enabled).