"I'm sorry, but these are the rates I offer to non-profit agencies. Please understand that these rates are already much lower than my standard rates and as such, are non-negotiable. If you decide to pursue either of the two solutions we have discussed, contact me and I will be glad to help you at the rate I have given you.
I wish you nothing but the best in the future.
Regards,
Name"
Something like that? Honest, polite, but to-the-point.
I believe that this method offers another benefit:
That the organization is a nonprofit does not require their team to be pleasant employers. Responding in such a manner as described by atgm allows you to judge their character a bit better. You're being respectful of their needs, but firm in your own. If you get an angry, abusive response, then you know that you made an excellent choice in not choosing to work for them. If you get a polite, understanding response, then perhaps you can bend your rates slightly, as they may be a better customer than you initially believed.
I wish you nothing but the best in the future.
Regards, Name"
Something like that? Honest, polite, but to-the-point.