The witch is glad that Dany's son will not become a khal and conquer for conquering means destroying. She does not see Dany as doing any favor of saving her from rape for she was raped 3 times prior that day. Thus it is seems a minor logical leap that the Witch could have tried to infect Drogo when she bandaged him up. Mirri Maz Duur last words were "The Stallion Who Mounts The World will never burn any cities. No nations will he trample into dust."

At the same her religion literally sees all people as one people before god, and in that religion she was a priest and healer. Thus it is rational for her to try to heal Drogo, while at the same time if he doesn't get better then it is her God's will that Drogo died. Furthermore it is not through her actions that Dany's son is sacrificed to saved Drogo, Dany made the choice to use blood magic. Jorah Mormont brought Dany into the tent even though it was commanded that no one should enter else dire things will happen. Thus you can argue it was not Mirri Maz Duur who killed Rhaego but instead Dany and Jorah. Now Mirri Maz Duur is still a snake for she did not tell Dany truely what she would gain (Drogo would return a husk of a man with no soul, Rhaego would be sacrificed, and friends would turn on friends and blood would be spilt.)