Yeah, I wonder if we need two paradigms here. Clicking things should only be for non-executable read-only stuff. And we need another UI verb for when we want to execute code, read/write, etc. Hard to get people onboard though, when they're just used to doing it one way.
The primary issue for me is that in protected mode, you can't copy to clipboard. So I can't take a note and send it to someone, I can't paste something into a ticket system, etc etc. I have to admit I'm pretty used to just clicking out of protected mode.
Word exits protected mode just to print. Apparently you can create screen pixels from that mode, but not if they're going to end up in a PDF or on paper.