You won't have any problems at all. Turkey still refuses to recognise Cyprus but they do not refuse entry to people who've been there. These days they even allow Cypriots to visit Turkey (done it last March), although since they refuse to accept Cypriot passports they stamp a piece of paper at the airport instead.

As for crossing over to/from the occupied areas of Cyprus (in case this is of interest), please see my other posting at:

http://www.flyertalk.com/forum/showthread.php?t=457085

Enjoy Cyprus :-)