If we need specialized behavior, we should build applications on top of bitcoin, and keep bitcoin stricly as a network protocol. Much like we don't define any website related standards in TCP/IP. We build over it.
If the ambition is to make bitcoin a backing of other _distributed_ crypto currencies, then I can´t see how this can be done without changing the protocol on the lowest level. This will be like transferring from single- to multi thread programming (each blockchain being a thread).
The general idea is:
1. A signal for transaction is made in the main chain (bitcoin) for transfer to the alternate chain (borgcoin), this can be verified by any miner of just bitcoin. The bitcoins concerned are subsequently transferred to an address with defined borgcoin escrow from where they can't be transferred in any other way than in 4.)
2. This is picked up on a miner holding both bitcoin and borgcoin, registering the transaction in the borgcoin chain to the designated address there (something like making 10xborgcoin from the bit coins).
3. Any disenchanted holder of borgcoin can then, after the rules defined locally in the borgcoin chain, register a transfer back to bitcoin, like "I want 1 bitcoin for my 10 borgcoin". He presumably also has to register this request in the bitcoin chain as a token transaction to make bitcoin miners aware what is going on in the borgcoin chain.
4. Any bitcoin miner holding _both_ the borgcoin and bitcoin chain, can then process the transaction from 3. out of any escrow account made in 1. This step will create a serious danger for forking of the bitcoin block chain. But I hope this danger can be averted by precautions like only allowing this kind of sync transactions to occur one day every week or so, when blocks with "borgcoin" sync transactions are to be preferred.