This sounds a lot like a pull down assay. If you are over-expressing tagged proteins (which greatly assist in pull-downs), I agree with jerryshelly1 above - you can immunopurify them first and then use the purified protein as "bait" for lysates in your assay. The approach you've described is a quick/dirty variant of the same assay. It might work, but it isn't very physiological. Is there any reason you can't either purify the protein, or express both proteins in the same cells?
As a positive control, I think you'd still want to show both recombinant proteins interacting in vitro. Co-IP's are nasty in the way they can fool you (both erroneous positive and negative results are common), so make sure there are appropriate positive and negative controls.
Edited by miST32, 11 March 2014 - 06:50 PM.