This will an even bigger issue with the mobile format, where keyboard controls are unavailable. For a method of one-click-to-pause to be consistent between desktop and mobile clients, having an on-screen pause button in the form of the clock is really a pretty good compromise.
The reason it was removed was that it was found to be unintuitive by users - they didn't realize that pressing the clock to pause was an option. And I suspect that players may indeed find themselves confused if they see a pause button in the pop-out bar but find their game suddenly paused because of an accidental click on the apparently-unrelated clock.
The solution would need to at least involve changing the appearance of the clock in case of a click, to reflect the paused state, while simultaneously reflecting the change in the actual pop-out pause button. But if a clever designer could come up with a graphic that actually looked good and looked like both a clock AND a pause button... that would go a long way toward settling this issue once and for all.