What are you talking about, joining head-to-head? You are aware that chromosomes have two strands of DNA, right? Like this:
5'--------------3'
3'--------------5'
I think that what you are suggesting is that this happened:
5'--------------3'3'----------------5'
3'--------------5'5'----------------3'
Instead of the proper:
5'--------------3'5'----------------3'
3'--------------5'3'----------------5'
If that is what you are suggesting happened, I am curious as to why you think that. It wont happen that way. Why do you think that the first chromosome wouldn't just twist a very little so it would match up and fuse? That is exactly how they form chiasmata.
Here's your link.
The hypothesis is that human chromosome 2 is a fusion of 2 primate chromosomes joined head-to-head.
The 5' to 3' structure makes this impossible, yet the problem is glossed over in favor of 'banding pattern' similarities (which mean nothing).
http://www.evolutionpages.com/chromosome_2.htm
If you twist the chromosome, you join the anti-sense strand to the sense strand and the anti-sense strand does not code.