You have a point, it would be disruptive. I believe it's the right move for the long term but there may be a better way to approach introducing it - suddenly cutting out any deductions for charitable giving would likely bankrupt those charities before government subsidization or non-tax deductible giving could pick up the slack, for instance.
Agreed, it would have to be phased in/out over time in a very smart way to not crush businesses and accountants. Doable perhaps over a long span of time if everyone agrees to it but man would it be a longshot. I'd imagine it would still have devastating second and third order consequences that aren't apparent until it's too late.