To make you feel somewhat better, I also just purchased a e46 about 2 weeks ago ( 323i ) and the clutch was replaced about 5000 km prior to my purchase , have all the receipts from BMW dealer to prove it. The clutch pedal does grab high, almost at the tip of the pedal just as you mentioned. It doesn't really bother me I just don't press the pedal in all the way
Replace the fluid, hopefully maybe that will help you out, or try to install a longer "clutch stop" as mentioned in the previous reply's.... Also you can always replace the clutch with an aftermarket one.
Ohh yeah, one more thing:
Clutch Stop DIY: