we need a system in place to blacklist/highlight any addresses that are linked to any coin theft - with the blockchain the coins should be able to be tracked down to an end address.
No we don't. That's a silly suggestin that would destroy currency's fungibility.
On the topic, I'd surely like if the pool operators reimburse users at least partially. There are options like gradual reimbursing from fees or sort of.
Though if it doesn't happen I'll be fine cause I didn't lost much thanks to my careful risk management. Still I won't ever deal with these guys.