I played quite intensively with iBA when it first came out around three years ago, exploring all the functionality. I've pretty much not touched it until this new EPUB3 option just appeared – but I vaguely seem to recall that the issue of the cover display not pausing to allow everyone to admire your work occurred then too. So I don't think that's new behaviour. (I'm not defending that design decision, I'm just saying…)
In fact, I've just double-checked several commercial purchases I have available and they exhibit the same behaviour. (NB I'm viewing these books on the iPad version of iBooks, not on my iMac version.)
On the iPad, the nearest you can come to pausing the full sized cover display, that I have found, is on the way back out. Get to the Table of Contents page. Then do a slow two-fingered pinch, pausing at the end of the pinch. You'll see the full-sized cover for as long as you keep your two fingers pinched together.
I think that's going to be as good as it gets.
...
The only workaround might be to replicate the cover as a bitmap on the first page within the eBook. I've just found a couple of books where I'm pretty certain that's what they've done.