An alternative using splits and joins.

$ perl -Mstrict -Mwarnings -E '
my @strings = (
   q{auth_plugin_stack = EXT::USCC::USCCAuth},
   q{auth_plugin_stack = a,b,EXT::USCC::USCCAuth,c,d},
   q{auth_plugin_stack = a,b,EXT::USCC::USCCAuth},
   q{auth_plugin_stack = EXT::USCC::USCCAuth,c,d},
   );

foreach my $string ( @strings )
{
    my( $left, $right ) = split m{ = }, $string;
    say join q{ = },
       $left,
       join q{,},
          grep { $_ ne q{EXT::USCC::USCCAuth} } split m{,}, $right;
}'
auth_plugin_stack = 
auth_plugin_stack = a,b,c,d
auth_plugin_stack = a,b
auth_plugin_stack = c,d
$
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I hope this is of interest.