The second sentence is correct. "I wish it didn't come to this" has a meaning of, "It comes to this [present tense], but I wish that it didn't." To refer to things that happened in the past, "to wish" is followed by the past perfect tense: "I wish it hadn't come to this." That is, "It came to this [simple past tense], but I wish it hadn't [past perfect tense]." I hope that this helps!

They both sound fine to me. I think there is a subtle difference between the two though. I wish it didn't come to this. (there is an emphasis put on the current state of things. Something went wrong but it's really the present that we care about.) I wish it hadn't come to this. (there is an emphasis on a series of events in the past that collectively led to the current state of things.) I hope this answers your question. I am curious to know what other anglophones think.

The second sentence is the correct one.