There is basically no reason other than they didn't think it through. Like much of paladin's stuff.

In 1.0, Holy Succor (paladin's native healing spell) didn't break combos, but Cure (cross class) would. Made sense I guess - that's the benefit of a native spell. Clemency interrupts our combos now because they probably just didn't think of it. The long cast time and interrupt vulnerability are maybe because they wanted to make it worse in some ways than a real healers' spells, but yeah they don't really have that problem with stuff like Maim or Fell Cleave. What's so powerful about Tempered Will that it needs a 3 minute cooldown? Why is Cover a 2 minute cooldown? A lot of it seems like just arbitrary decisions.