A few weeks ago a merchant that sold an item for $100 dollars worth of bitcoins got paid about $100 dollars worth of bitcoin.  If that merchant then used those coins for making purchases or cashed them out, that merchant got about $100 dollars worth of value from them.

Today a merchant that sells an item for $100 dollars worth of bitcoins gets paid about $100 dollars worth of bitcoin.  That merchant can then use those coins for making purchases or cash them out and that merchant will get about $100 dollars worth of value from them.

What is the difference for the merchant between the situation a few weeks ago and the situation today?

Now if you are saying the merchant may not want to hold bitcoins at this higher valuation because the risk of the exchange rate decreasing, then there are methods for merchants to hedge, such as buying PUT options or to sell futures contracts on ICBIT, so that the merchant can "lock in" at today's value yet still hold that value in the form of bitcoins.  

Ideally though, the merchant will have vendors, employees and investors to pay so that bitcoin revenues can be used for that spending rather than simply getting cashed out to fiat as part of each transaction.