You could use look-behind (?<= ) and look-ahead (?= ) expressions to look only for quotes which are not beside a comma or at end and start of the line:
s/(?<=.)(?<!,)"(?!,|$)/\\"/g A simple test in the command line brings me:

user@machine$ perl -pe 's/(?<=.)(?<!,)"(?!,|$)/\\"/g' 
"call from "friend"","call from "friend"","call from "friend""
"call from \"friend\"","call from \"friend\"","call from \"friend\""
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The 2nd line is input, the 3rd output.

Looks good for me. Some special cases with escaped commas inside the strings might not match correctly. You should check this.