I think that this is generally normal. A lot of people notice this and have commented on it:
http://986forum.com/forums/general-discussions/35443-stiff-clutch-clutch-replace-q.html
http://986forum.com/forums/general-discussions/37300-2003-boxster-s-extremely-stiff-clutch.html
http://986forum.com/forums/general-discussions/6582-extra-stiff-clutch-question.html
Compared to my Porsche 996, BMW 325i, Mini Cooper S, and Miata, the Boxster's clutch is by far the stiffest of all.
Of course, its hard to gauge "stiffness" over the internet and impossible to know if your car is well beyond normal stiffness, but if the shop thinks it ok, you're probably ok.