I also think that it's better to have some Condition block that checks whether some Variable equals to true/false or 1/0... or something else.
If you have fully disconnected blocks, they are excluded from the output file. In your case this will happen, I believe. The EA generator does not check the contents of the Run block. And so many blocks to turn on/off... I think it's too much and you are doing something in the worse way.
Just in case, if you have a group of blocks and you want to prevent that group of blocks to work, it's enough to turn off only the block on the top (if there is only 1 block on the top). If the block on the top doesn't have the chance to pass, then the blocks below will never pass, even if they are not disabled.