Krishna has never accused Pratigya of anything, after his initial anger...even then he said 'how could I belive that someone like angad would let you go without touching you'.......
The main problem between Kriya is the believe that she has lied constantly. Trust is gone. This is what needs to be rebuilt.
There is nothing for him to realise he has misunderstood pratigya over, even she has said 'it is not my fault'....it is the fact she lied and therefore betrayed his love is what his current anger is all about. Some people are also saying Krishna will tell Aarushi not to tell Aman about what Shakti did.
Again, No. This will be against his character and we all know, after his own betrayel by his wife, he would be the last person to encourage someone else to lie to their husband. Remember he told prats to tell aarushi to reveal her secrets to her husband before the marriage because even an educated man won't like being deceived.