It takes 5 lines of code to implement as an option. I've also set it as enabled by default.
I'd also say that yes, myself, I'd currently prefer this off. This may be just because I'm used to having it off, and after giving the new system a chance, I might change my mind.
The obvious argument for restart still counting is that one may assign a skill to a pre-placed lemming on a very early frame; without pausing in such a case, it would be very hard to overwrite this. I have some longer-term plans for dealing with this kind of matter and lots of other replay manipulation issues in general; but these are not going to make it into the next stable release.
For this upcoming release, I'll leave it as an option (with current behaviour), and based on feedback from people using it, I'll see what changes might be made for later versions.