I think the conflict is that if one views bitcoin-plus-sidechains as being an economic system, then "just don't use it" is not a valid response to the concern that the system as a whole is being destabilized. Events in one part of the system may have consequences (including unforeseen consequences) in another part of the system.

As you say, it may be that side chains are implementable within the current bitcoin system without changes, in which case, this is inevitable. This is certainly true for some sort of bitcoin-backed-coin model that involves some sort of trusted intermediary/intermediaries (what the paper calls the federated model). Nothing prevents someone from making a bitcoin-backed-altcoin any more than a weed-backed-altcoin. Putting aside the rather large issue of backer trust, this is equivalent to a side chain.