At least we know that the alts are in place therefore we should at least get those back.
That's not guaranteed. It didn't happen with Mintpal - some people got their other coins back but many didn't. For all we know the thieves may have access to other hot or "cold" wallets and just may be shifting the bitcoins first. Or the people at BTER may be desperately selling what they have left in other wallets so they can get away with some money and start again (assuming it wasn't an inside job anyway). Would be interesting to know how long they knew something was wrong.