Yes, you would most likely see a difference with your bottleneck issue if you upgraded to 7200rpm drives. But with the system being a Mac Pro, you could easily set your raid up as a RAID 0+1 which would give you the benefits of redundancy and speed.
See article:
http://www.pcguide.com/ref/hdd/perf/raid/levels/multLevel01-c.htmlIf you set it up with 2TB drives for each drive bay, which could be done fairly inexpensively you should see a substantial difference in speed and you would not have to worry about remembering to manually backup your data (not that I am suggesting you don't from time to time.)