The reason I chose the shorter chain was because all of the main nodes including cryptsy and coins-e and the two main block explorers were stuck at block 785863 and reporting that specific block as being invalid. Whoever made the invalid block probably did so on an old wallet before the kgw timewarp fix. Some of the pools accepted it while most of the wallets didnt. By the time I released the fix to get cryptsy syncing again the chain autocorrected and orphaned the longer chain anyways. Why did it do that? Because only a few of the clients were actually accepting it.
So what was the right answer? Allow an invalid block by putting in an "ignore block 785864 it may be invalid but who cares" or orphan a days worth of work to make sure the block chain syncs fine and does so by staying true to the parameters we all agree on.
Altexplorer.net was on the wrong chain, it may be longer, there were a couple pools on the longer chain but it was still an invalid chain, if you dont believe me, set up 2 nodes on a private network with the other chain.. have the one node already have the wrong chain but start the second node from scratch and you will see it doesnt sync past 785863 then check the log and you will see why.
FRK was stuck for 37 hours before anyone noticed, cryptsy needed a fix asap or risk being delisted. So again, what would you have done? I'm sorry some people lost work, I dont have any money to compensate, wish I did but the only option we have is to move forward. We need to do whatever it takes to stay moving forward even if it means to step back a couple steps and correct a problem.
Apparently Cryptsy is on the long chain now... and my coins are toast....