Confusion between "did Bitcoin fail me and lose my coins or did a Sidecoin fail me and lose my coins" is a very legitimate issue. I'm worried about this also.
I think a lot of side chains will be seen as services beyond the main chain. For example today if one wants to anonymize coins they need to go use some sort of mixing service, if they lose their coins in the process the service takes the blame though, not bitcoin. I think sidechains will be the same, people have bitcoins and then decided to use some anonymous sidechain service, if they lose their coins I think it will be clear it was the sidechain / service at fault.
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.
Sidechains are like Bitcoin companies/services. If you decide to trust some shady one because it promises unconvential returns or features then you expose yourself to the underlying risk that they disappear with your money.
When we get to "ordinary people" using Bitcoin, established sidechains that have been carefully reviewed and vetted by the community will be available and should serve any conventional need that a consumer might want. My guess is that at this point they are not even referred to as "sidechains" but Bitcoin "applications" or services.
If one decides to step outside of this "safe" environment and experience more obscure services/sidechains then he should proceed with caution much like he should be doing when dealing with less renowned companies.
I can always blame Bitcoin companies/service, but how do you hold a decentralized P2P MM SC responsible, when you are entrusting your coins to a decentralized protocol run on p2p network, not a Bitcoin companies/service, in this scenario SC failure is a Bitcoin Failure. if you are introducing billions of these SC, companies will try to reduce liability by issuing a SC MM independent prototypical - "they dont make mistakes it was a fault of the protocol", the risk of failure grows exponentially as more SC come on board. Alts are not a treat anyway, the goal is may the best money win, and bitcoin is such a quantum jump from what we had, Alts are an incremental improvement.
If there are billions of these SC as you say, the vast majority will be so small that the failure of any one would hardly even be noticed. Today there are tons of bitcoin website services and lots of them have gone down/disappeared/etc. Most were so small they were not noticed (I'm speaking to you betsofbitco.in)