I think it is a problem that you can never really trust that the chain will not be massively invalidated, and replaced by a longer one.
This is an issue for all but the largest instances of bitcoin. A global widespread bitcoin system wouldn't have this issue, but anyone else would.
If a small country, say Luxembourg, started a bitcoin instance for themselves, they would never know if the German or French government would be hiding a longer chain, just in case.
These are simply good reasons for not starting your own little separate independent bitcoin chain. For the best security stay with the main big chain. Instances such as yesterday's should be so rare you don't need to worry about them. The problem of being out powered by some other big entity is well understood and is minimized by staying with the biggest bitcoin chain there is.
Note that the current bitcoin net is still tiny and you shouldn't really rely on it yet for anything serious in my opinion.