Why yes, actually
You won't get a BMW S1000R shock to work properly on the FZS600, it's just too long at about 325mm and the damping is way too soft as a result :
http://foc-u.co.uk/index.php/topic,17655.msg203848.html#msg203848. Having said that, the latest version of the shock is about 10mm shorter and might work ok but I haven't tried it myself.
Your options in order of cheapness are:
1. 2001-05 FZS1000 rear shock with 600 spring fitted. Plenty around and better than standard 600 shock. But there's a reason most 1000 owners dump them ...in favour of an R6 shock.
2. 2008 onwards R6 shock. Best value adjustable shock but as you say, little scope for raising the back-end too much, certainly not much more than an inch over standard height.
3. Aftermarket. Plenty of choice here. At a price...