This is a little difficult for creationists to explain away although they have found a way, AiG has written an article in response to the argument by Kenneth Miller. This version of the argument is from a video by Eric Hovind and Jonathan Samson, Samson gives the argument;
So it we strip away the bias and just look at the facts (as everyone should),
the facts are; yes it seems like humans have experienced fusion in the past in
human chromosome number two. But what does that mean? [Hovind cuts in to say
"That's how--there interpreting it--as evidence of evolution"] It means they're
attaching it to their own story.
So essentially he is saying that we are assuming that humans evolved from apes before we look at the evidence and have misinterpreted it as evidence of common descent. Of course is this accurate? Evolution gave a plausible explanation of the missing chromosome and it has turned out to be true. Also since it resembles two ape chromosomes and it predicted by the theory of evolution it doesn't seem too far fetched to say it is evidence of evolution.
This argument is not filled with the usual crass scientific ignorance that usually accompanies Hovind arguments, but it still does not succeed. I think creationists have a point with worldviews affecting how we approach science but they take it to the far flung extant to try to force-fit scientific data into their narrow, flawed interpretation of the bible (which they somewhat arrogantly equate with the biblical position). Christian or non-Christian, one can not accept such an extrapolation.