didn't read anything except first post, but I don't think anyone mentioned this
Well it's not just about physical defense. Most of the arcane classes' defense comes from RPD actually. If you are switching to DD mode then I can assume that you're using attack gear (with -channel/magic add-ons on armor and attack level/magic engraves on accessories).
So naturally you are losing out a lot of survivability in comparison to regular support gear.
Buffing the base defense of arcane classes would unbalance their def in regular, support gear, making them much more difficult to kill in PK. So the DD clerics can't be really "fixed" without breaking something else.
Also it's not a problem of clerics specifically being nerfed. All the arcane classes got pretty much the same gear with the same addons and nearly the same set bonuses. So the only aspect which is making physical defense of these classes different are their own buffs. For example wizards and venos in fox form got the highest phys def, while physics and venos in human form the lowest.
Clerics got their vanguard shield which is not helping a lot if you're using the full attack gear.