Easy. You do it before you turn them into an array of hashtables … 
$List = @'
"fqdn","bla"
"this.domain.com","blu"
"that.domain.com","ble"
"some.domain.com","blo"
"that.domain.com","bli"
"this.domain.com","blö"
"some.domain.com","blü"
'@ |
ConvertFrom-Csv -Delimiter ',' |
Sort-Object -Property 'fqdn' -Unique
$thiscertSANs =
foreach ($entry in $List) {
@{dns = $entry.fqdn }
}