PietLT It can't and won't remove the file from your mods folder while the game is running, but yeah having a quick way to re-enable all the hacks would be nice.
Currently, you can work around the re-enabling hacks part by saving a profile first:
.enabledhax save-profile pre_disable
Then disable and re-enable Wurst as you normally would.
Then:
.enabledhax load-profile pre_disable
To make this easier if you do it often, you can give the profile a shorter name (mine is just alex) and/or set up keybinds for the .enabledhax commands.
Hope this helps!