As long as they are very clear about what they are doing I don't have a problem with fractional reserve in principle, but if exchange owners are doing this to trade on their own exchange to the detriment of other users then surely people would just move to a different exchange?
If a business wants to engage in fractional reserve practices then they need to offer something to their users in return for taking the risk of allowing the business to do this, like interest payments or something. That way people can choose - play it safe by using a service with no fractional reserve or take a risk on trusting a business with their coins in the hope of getting a share of the profits.
What most exchanges that are likely operating on a fractional reserve are likely doing are spending their customer money. What a "real" fractional reserve exchange should do is use a portion of customer deposits to
lend money to borrowers with the hope that, after interest payments and customer defaults, they will have a net profit on their loans.
Exchanges could lend these coins to themselves to short the market and trigger speculator's stop-loss. Since they have all the customer's coins on exchange, based on FRB principle they could borrow 90% of the coins, they could greatly crash the price to wipe out everyone, because no single big whale have the amount of capital to deal with all the coins on that exchange (Whale's money is only part of that pool)
For example, an exchange have 50k coins, and the amount of fiat money on exchange is 25 million, which maintains an exchange rate of $500. Then exchange borrow 45K coins to themselves and short the market, so all the fiat money on that exchange will be quickly drained, and the exchange rate could cut by half or more
Then the bargain hunters will rush in to deposit and buy coins to withdraw, money arrives after several days, exchanges will soon find out that they are facing a much larger withdraw than 5K coins (the rate under normal market condition), that will dramatically reduce their reserve and they have to buy back coins to reduce the withdraw pressure, then the price will recover quickly
Bitcoin world is wild west, no regulation on exchanges for what they can do