Most of the 'holes' mentioned have to do with contract developers writing buggy code rather than bugs with Ethereum / Solidity itself. That being said, there's likely holes that aren't discovered yet, but the title and article is a bit misleading in that it points to flaws with Ethereum itself.
Sensationalist title. The study found vulnerabilities in 34,000 out of 1,000,000 contracts. That's less than 4%. Hardly surprising for a new technology.
Ethereum has already forked into Ethereum Classic, due to an exploit 2 years ago. Maybe it will fork again... Ethereum Classic2?
This is a first iteration of technology. Early connected computers and internet routers had security problems too. That didn't stop evolution.
I don't see what could possibly be the long term issues with a decentralized version of Windows XP handling global currency exchanges.
There was nothing wrong with Ethereum's implementation of smart contracts, just Parity's source code for multi-sig wallets.
Quantstamp is in the process of building a decentralized solution for smart contract verification.