Thanks argv0 for your explanation. Being able to see new messages is important. If you are going to kick someone, but they apologize in their next message, and your window is frozen, you won't know he or she apologized. Perhaps kicks and apologies are both more rare than I'm estimating.
Accidentally kicking someone because they "apologized" too late is much less of an issue than trying to right click on a nickname during an enormous message flood to kick a user.. or trying to op a user only to realize you clicked on the wrong name because your window scrolled.
The evaluation behaviour is correct, by the way. It would be at least a million times worse if the target could change after showing the popup.
As for options, Khaled had previously pointed out that he's trying to pair down the amount of trivial visual options mIRC presents rather than add more. I can't speak for him, but I personally don't think we need to add a toggle switch for every single visual change in mIRC. The application behaves the way it does... rather than trying to fight it, perhaps you should look for another way to do what it is you want to do within the constraints of the program you're using. Not keeping popups open for minutes at a time would be a good start. That way channels won't start scrolling while you are deciding what it is you want to do. And if you really do want a more modeless behaviour, use a HOTLINK script to open a @window at your mouse on an rclick instead of relying on popups at all.