I downvoted you because - while you raise a generally valid concern - your statement is exaggerated to a degree that makes it grossly misleading. You say:

> which means that they could make arbitrary changes to the blockchain

This makes it sound like the 51% attacker could make arbitrary changes to the ledger, thereby stealing arbitrary shares. That is not the case. For example, such an attacker cannot forge any signatures and thus cannot manipulate transactions. All the attacker can do is censor new transactions or slowly unroll past transactions. In case of 51% of the computing power, unrolling could happen at a speed of (51% - 49%) = 2% of time, i.e. if the attack lasts for 50 days, the attacker could unroll one day worth of transactions. What makes the unrolling problematic, is that it enables the attacker to double-spend. One potential measure for NASDAQ to prevent this is to demand known signatures to be used for transactions (i.e. whenever you transfer shares, you must use a signature you previously registered with NASDAQ). With colored coins, the issuer can enforce such restrictions by refusing to redeem shares that were not properly obtained. So even in case of such an attack, NASDAQ could identify the attacker (or the person collaborating with the attacker in order to attempt a double-spend) and initiate legal measures (i.e. sue the attacker for damages).