First off, do not upgrade the HD when you order from Apple. Apple charges way too much for RAM and hard drives.
Next, you think $50 is a lot to add an option to a $2,800 machine? Why would Apple include wireless in a Pro tower? If a company decides to buy a bunch of MacPros and doesn't want to use wireless (which most companies would not), why should they pay extra?
You only need to add the wireless card if you want to connect wirelessly to the network. You can connect an ethernet cable from the MacPro to the wireless router if you don't want to spring for the wireless card,