The Republic got along just fine, with respect to this issue for, what, over 150 years without a Johnson Amendment.  I can see no logical reason to give up free speech rights in order to perform charitable works.  That being said, I do think that fear of prosecution pursuant to this amendment is perhaps, on balance, good for churches, for the danger of divisions mentioned here in the comments.

On the other hand, a regulation which exists, but is never actually enforced, seems like a bad thing.