I agree with you.  Obviously, it is preferable to have a complete gift letter for a restricted gift, so that both parties can be clear on what is expected.

But one of the important responsibilities of stewardship is not to waste the organization’s money or reputation on silly disputes with donors (or their heirs).  If a donor has taken the time to check a box for a specific use, or to note a specific use or restriction on the memo line of a check, one ought to assume that the donor meant to do so and consider the instruction as a restriction on the gift.  If the information is not clear, the organization ought to clarify with the donor what was meant.  If the organization does not want to live with the intended restriction, it ought to ask the donor to waive it.  In any case, it ought to document the outcome of the discussions, with the donor’s written concurrence if possible.

Even if your professional fundraiser were correct and the instruction was not legally binding, it wouldn’t be very good donor relations to ignore the donor’s wishes.