I think so. A huge amount of energy is now trying to get to ground. Power will now be dissipated across the ground (so, from the lightning rod to the earth). This is bad ("ground" is no longer at ground potential everywhere), but probably not as bad as the alternative.

I think one way to think about it is that, ideally, ground is a single point in a circuit that is defined to be at zero potential, always. Anything that appreciably violates this assumption causes bad things to happen, though often the bad things are subtle/not that bad (e.g., your guitar amp starts buzzing more than you want).