Stealth fix! I saw this on Elitist Jerks, and had to see for sure:
Happily, Holy Word macros work normally now.
For realsies? Yep, sure enough I tried last night using a basic mouseover macro with clique:
/cast [@mouseover] Holy Word: Chastise
And it worked! Now, you might still have to have the chastise spell somewhere on your action bars (that has always been a precondition of this macro), but indeed, no more weird click workarounds. REJOICE!