Best way, if you have control over building the initial array, is just set things up like that at the start as you add entries.
If not then build a temporary array to sort:
foreach ($input_arr as $key => &$entry) {
$level_arr[$entry['level']][$key] = $entry;
}
Leaves you with the form you wanted and everything referenced together.
Build the array like that in the first place though if at all possible.