You could argue that the ease of desecration is part of their balancing - do I actually bother with so and so or do I desecrate him. I think i got more EM desecrations then times I've worshipped her, and I actually LIKE her, and have been using her forever, even before all the buffs. I actually prep a salve on just about any run just because of the chance I'll run into to the "free 25 piety and 3 indulgences" bonanza that her altar presents.
Wonder what would happen if Taurog slapped a crapload of weakening on you for his punishment? Big enough stack to discourage newbies from even thinking about it, but it would let pro's think of the altar as "spend gold on green potion, get a nice piety windfall, a few indulgences, ad actually us EM this time around". Would solve the original problem.