add_action( 'wp_default_scripts', function( $scripts ) {
    if ( ! empty( $scripts->registered['jquery'] ) ) {
        $scripts->registered['jquery']->deps = array_diff( $scripts->registered['jquery']->deps, array( 'jquery-migrate' ) );
    }
} );

// silencer script
function jquery_migrate_silencer() {
    // create function copy
    $silencer = '<script>window.console.logger = window.console.log; ';
    // modify original function to filter and use function copy
    $silencer .= 'window.console.log = function(tolog) {';
    // bug out if empty to prevent error
    $silencer .= 'if (tolog == null) {return;} ';
    // filter messages containing string
    $silencer .= 'if (tolog.indexOf("Migrate is installed") == -1) {';
    $silencer .= 'console.logger(tolog);} ';
    $silencer .= '}</script>';
    return $silencer;
}

// for the frontend, use script_loader_tag filter
add_filter('script_loader_tag','jquery_migrate_load_silencer', 10, 2);
function jquery_migrate_load_silencer($tag, $handle) {
    if ($handle == 'jquery-migrate') {
        $silencer = jquery_migrate_silencer();
        // prepend to jquery migrate loading
        $tag = $silencer.$tag;
    }
    return $tag;
}

// for the admin, hook to admin_print_scripts
add_action('admin_print_scripts','jquery_migrate_echo_silencer');
function jquery_migrate_echo_silencer() {echo jquery_migrate_silencer();}

// Set to true to prevent console output; migrateWarnings still maintained
// jQuery.migrateMute = false;

add_action( 'wp_enqueue_scripts', function()
{
    wp_add_inline_script(
        'jquery-migrate', 'jQuery.migrateMute = true;',
        'before'
    );
} );

// Show a message on the console so devs know we're active
if ( window.console && window.console.log ) {
    window.console.log( "JQMIGRATE: Migrate is installed" +
        ( jQuery.migrateMute ? "" : " with logging active" ) +
        ", version " + jQuery.migrateVersion );
}

console.clear();

<?php
/**
 * Disable jQuery Migrate in WordPress.
 *
 * @author Guy Dumais.
 * @link https://en.guydumais.digital/disable-jquery-migrate-in-wordpress/
 */
add_filter( 'wp_default_scripts', $af = static function( &$scripts) {
    if(!is_admin()) {
        $scripts->remove( 'jquery');
        $scripts->add( 'jquery', false, array( 'jquery-core' ), '1.12.4' );
    }
}, PHP_INT_MAX );
unset( $af );