If they'd keep BTC balance, it wouldn't ease up any hurdles - the AML&other compliance issues aren't set by banks, but by regulations which apply to everyone doing significant amounts of trade.
If the merchant receives the funds in a fiat currency account in a bank, then the bank worries about AML and related issues so that the merchant wouldn't have to do that - receiving money to a regulated financial institution exempts your business from most of these regulations, but if merchants such as NewEgg, Expedia, CheapAir and others would accept BTC "directly", then the same rules as for cash transaction would apply, namely, they are responsible for ensuring that high value transactions or repeated low value transactions that add up to a lot of value cannot be anonymous, they become responsible from enforcing KYC (know your customer) requirements, they become responsible for any laundering done through their channel if someone finds a way to do this, etc.
The only way how a legitimate business can deal with cryptocurrency (or cash) in large volumes is if they can ensure that the expected benefits of cryptocurrency (unrestricted ability of anonymous/pseudonymous trade) don't get used. The only high-value goods that get sold/bought with BTC are illegal items. The regulations don't affect selling coffee for BTC (but high transaction fees do), but if you want to do serious transactions - transfer wealth, buy lots of electronics, cars or real estate, settle financial deals or stock purchases - then that won't work with anonymous cryptocurrency unless you have appropriate paperwork documenting how you got it, or are ready to pay extra tax (you know that if you bought BTC for $10/coin and sell it for $1000/coin, then the difference is taxable income, right?). It's the same manner as allowing your customers to pay for stuff with a briefcase of cash - you can do that, but you'd need to report the transaction, identify the customer, and that customer would either have a clear source for that briefcase of cash or would have a talk with IRS.