You'll have to use your own iCloud account with a different Apple ID to avoid ending up with merged contact, calendars and any other data you both sync with iCloud. To do this on your phone, go to Settings>iCloud and turn off syncing for contacs and anything else you are syncing, when prompted choose to Keep the data on your iPhone. When done, you can scroll to the bottom and tap Delete Account. Next set up a new iCloud account on your phone with a different Apple ID, then turn syncing back on for contacts, etc. in Settings>iCloud.
At this point you will both have to go to icloud.com, sign into your respective iCloud accounts and manually delete the contacts you don't want you your respective phones. (No way around this.) Do the same for calendars if those were merged. Once finished you won't have the problem again.
FYI, you can still share your iCloud calendar with each other if you wish even if you have separate iCoud accounts (http://support.apple.com/kb/PH2690). You won't, however, be able to share Photo Stream photos until iOS 6 is released later this fall (see http://www.apple.com/ios/ios6/#photostreams).