I think you are misinterpreting that paragraph; and thus not giving Microsoft their due credit.
It is saying that Microsoft already does run a ‘donation’ program to NGOs that likely does allow them tax deductions at no cost. But that’s not what this is. By instantly creating a license that any NGO can use for free; they cannot claim a deduction. For a deduction, they would have to get the NGO/journalist to go through specific channels so that they could document the ‘donation’. And that of course if why they want to move people to their donation program.
This is talked about in a bit more detail in the Microsoft blog entry that announced it. I would expect this to make it a bit more difficult to get NGOs to use their donation program since the motivation for jumping through the hooks is less.
This is a fantastic program and Microsoft should be commended for it. Even on Slashdot.
Now, getting deductions for software (or other IP) donations in general is ridiculous and something that governments should reconsider. Any business deduction where they can control the value of the donation by their pricing is somewhat shady. But this license does not seem to be taking advantage of that.