I don't know what the opinions are now-a-days, but last I heard the reason for the rule about not fighting on holy ground was a practical one.
When immortals fight, they both release quickening into the surrounding area. If neither die, they both regain their quickening, but if one dies, all the released quickening goes into the winner. However, if the fight is on holy ground, then the holy ground itself draws in all that released energy, regardless of the outcome of the fight, leaving both immortals (or the winner in the case of one immortal losing his head) weaker then when they interned the fight.
As a GM, I would have both immortals put a one or two (the same for both opponents) fate points on the table. If they both live then they get their point or two back, if one dies the other gets all the points. If the fight is on holy ground then the outcome doesn't matter, those two or four fate points are lost completely.