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Better Formats is using hook_form_alter for a complete rewrite of the filter-selection in $form. Therefore the pingback input filter isn´t hidden any longer. The only solution is to change the weight of the pingback module in the system table (which changes the order of the module hooks).
Could you please implement the following code in the function pingback_install?
// Increase module weight to prevent compatibility issues.
$sql = "UPDATE {system}
SET weight = 200
WHERE name = 'pingback'";
db_query($sql);