In 2002 we published the results of a study of pair programming showing that using pair programming in an introductory programming course dramatically increased retention. Pair programming is now an NCWIT “Promising Practice” (http://tinyurl.com/pairprogrammingNCWIT).
In 2011, Salleh, Mendes, & Grundy published “Empirical Studies of Pair Programming for CS/SE Teaching in Higher Education: A Systematic Literature Review” in which they reviewed 73 studies (all but 4 published since our first report). One conclusion was that “Almost all studies’ findings reported that students’ satisfaction was higher when using PP compared with working individually.”
Just do it. I firmly believe any pair programming method is better than making them work alone and live in fear of being accused of copying if they talk to anyone about their program. You don’t need a complicated system. At the VERY least, make pair programming an option for those that want to use it.