As an e-commerce professional I personally consider it a negative value-add if the retail stores of whatever company I am working for refuse to match the price shown on the company e-commerce website. As a customer, this practice absolutely ticks me off to no end. Yet I seem to be running into it more and more and so are many others. The Consumerist website has many such 'horror' stories, including this one of a Best Buy that outright says up front, sorry, no website match for you. Of course, I'm sure a good deal of you are also familiar with Best Buy being caught, in the past, hosting a different version of their website, with different pricing, within their stores. So whether or not their assistance with helping you place an online order gives you any peace of mind is entirely up to you.
As for the practice as a whole, I understand cost of goods sold and the finances involved, yet what I don't understand is why stores are willing to alienate their customers' future purchases by doing this. For starters it adds confusion. Persons not as well versed in the retail environment will probably not understand why your website has the item listed as cheaper. Double this confusion if your website offers 1) free shipping and/or 2) in-store pickup. More importantly, you've just scored yourself a customer with a negative experience. We've already established the customer is already versed with the web (having figured out the price differences already), thus it's probably fair to assume this negative experience will be shared via facebook or twitter. As this customer is presumably at least partially web-savvy, he / she also knows how easy it is to just go elsewhere. Sure you might make a few extra dollars on that in-store sale, if I really need the item today. However, you can be sure that I'll think twice before coming back to you in either online or offline format.
While one negative experience and potential lost future customer might not mean a lot, think of that multiplied. Once mighty chains such as Blockbuster and Borders have either disappeared or are on the brink of doing so, because customers went elsewhere for whatever reason. As a business owner or manager, there are definitely lines in the sand you want to draw when it comes to customer concessions. This, however, I don't think is one of them. An unruly customer who asks for an unreasonable discount is one thing, a customer who simply asks you to match the price another division of the SAME company is already offering is a completely different thing.
In a perfect world online and offline prices would match. Please be sure to let me know when you find that perfect world so I can move there too. However, in the case where store price doesn't match the online price, a policy of just "no" makes little sense. If a customer checks out and pays your offline price, that's great. No harm, no foul. However, if they specifically ask to speak to a manager regarding the discrepancy, consider the positives and the negatives of the situation. You could be setting in motion a chain of events that will effect your future. Whether those events are positive or negative is largely up to you.