I am not convinced that you are yoitze matonos la’evyoinim with donations to moisdes. The mitzva is to give money to an oni. Yes moisdes are in desperate need for money, but they are not poor PEOPLE! You must give them mnoey on purim because of kol hapoishet yad noisnim lo, but you must still give money to poor people to make their purim a happier one!
The Halacha states that matanois la’evyoinim is so important that one should minimise in seuda and mishloach manos and give more matonois la’evyoinim.
I have seen – as others have mentione – people giving donations to a moisod and informing those they normallly send mishloach manos, that this year they have given a donation to tzedaka instead of sending so many packages. This fits into the halacha very well!