If a sidechain is integrated into Bitcoin-qt or blockchain.info to the extent that you're not even aware of the sidechain being used, then I can see the scenario you're describing as being confusing and damaging to Bitcoin. But I think SC's will be implemented in a manner that it is clear when they are being used.
At least that is my expectation / hope.
I share the hope but not the expectation.
When speaking with someone about Bitcoin and they have only been involved since maybe 6 months or so (started after all the gox events), and they say that they have some bitcoin, and then during the discussion you learn that their bitcoin are in their Coinbase account, or their LocalBitcoin account....
Do you then tell them that they are wrong and do not have any bitcoin?
How likely are they to believe you if you tell them this?
There are a lot of these people.
Most people think that the dollars they have in their deposit account at bank are theirs and not the banks too, and won't be convinced otherwise without a lot of work.
...and that they own gold if they have some GLD.
That's a great way to put it.
It also means the problem already exists today. What is different between coinbase failing and a sidechain failing. I'd propose very little.
When MtGox failed, a lot of the press said Bitcoin was hacked even though we know that wasn't the case. A SC failing will be very similar.
problem.