Then write better scripts. If you have to restart mIRC each time then it is poorly written. What you should do is something like this:

Code:
alias inittimers {
  ; Initialise timers here.
}
on *:start:{ inittimers }


Now when you want to start the timers, you can just type /inittimers without restarting mIRC.

My suggestion was that there should be an option to turn remote off when Ctrl+Break was hit, and genius_at_work gave one good reason why you might want to disable remotes (events being triggered with buggy scripts in them), so it can't possibly be a bad idea. If you don't want remotes disabled, then simply don't turn on the option.