I don't see any need to notify the user at all.
Well, since setting a script in devmode would prevent it from being ran as the latest script handling change has intended. it would make it a candidate to cause memory leaks etc.. Informing the user is therefore necessary. Otherwise is the latest script handling change possible to circumvent thus making it not to fix was it was intended to fix.
But if the dev's feel such a restriction is necessary, then perhaps enable only MM debug releases (but still no pop-up notifications)
Good idea. Another one could be to create strict developing version of MM. Which treats script the old way and has no pop-ups!
What if you had or were developing multiple scripts, can you imagine getting a bunch of pop up warnings every time you started MM? I would go insane and simply stop using/developing scripts.
The suggested change would almost eliminate the need for a restart so I really don't see this as a big problem!