Because it IS important. If a donation is deductible, then it does more good than a similar outlay which is not deductible. If one donates $50,000 then X good can be done. If one donates $75,000 because otherwise one would lose the extra $25,000 to taxes anyway, then 1.5X good can be done. By making charitable donations deductible, people are encouraged to donate more than they would otherwise donate because their overall cost (including taxes) relative to the benefit is reduced. They never have more money than had they not made the contribution, but they can give more money for less overall financial loss.
<sigh> I swear to G-d, people used to be smarter.
The lower the effective rate - no matter the cause - the more net money lost for the contribution. Period. Your net rate is lower because you gave away some of your otherwise taxable income, not because you've found some nefarious scheme to defraud the taxpayer.
EDIT: In your example, without the donation the entity is left with $650,000 after taxes. With the donation the entity is left with $325,000 after taxes. No one should ever be so abysmally stupid as to think the entity made the donation for financial purposes.