Ayesha and Malika are two different characters. Malika is obsessed with Milind to such psychotic extent whereas Ayesha was not so delusional. Malika lusts Milind and is attracted to Milind's image more than anything and doesn't know him enough to be IN love with him. Whereas Ayesha knew Milind from childhood she knew and loved the person he was. No matter how hard Ayesha tried Milind never betrayed his love for Prachi. So when Milind never succumbed to Ayesha's ploys then ye Malika kya cheez hai?!
Also Prachi promised that she would not be at peace until she put Ayesha's murderer behind bars. So if she does find out Malika's truth she will not agree to the deal of walking away from Milind. Prachi lives and breathes for Milind and vice versa so how could she walk away from that. Also she now has to think about her child could she risk her child not having the presence of its father. Prachi herself was close to her father and knows the importance of his presence also what effect the absence of a father has through Ayesha. So Prachi has many reasons to fight for Milind and put Malika behind bars.