I think a totally new alt coin should be created for zerocoin because that is lowest risk and barrier is lowest.
Many of you will laugh me off as paranoid, I approach these issues as a "think of the worst case" situation and prepare for it.
I think we will waste a lot of time and resources by assuming the worst case and preparing for that. It does not seem like a rational strategy to me.
The rational strategy would be to weigh risks and benefits, and adopt the solution that best balances these two aspects.
In the case of Zerocoin we have both a lot of added risk (the protocol hasn't actually been deployed yet),
and it increases the hardware requirements (CPU power, storage space, bandwidth) of running a full node.
Given that the benefit is, at best (ie. in case there are no vulnerabilities), full anonymization of all transactions, and given that this can already be achieved selectively by individuals who require this feature, I think Zerocoin should be implemented as a separate cryptocurrency, and tested out completely separate from the Bitcoin protocol.
I think a lot of people quickly forget just how unsafe Bitcoin was regarded as just two or three years ago. This would start all over again with a modification of the core protocol, and if you worry about a declining price of bitcoins, I believe modifying the existing core Bitcoin protocol would do
much more harm than a separate Zerocoin taking off. At the bare minimum it will take as long as Bitcoin has existed for people to trust that protocol, and probably longer because introduces more complexity into the core protocol.
In other words, I don't think we are in a hurry. Zerocoin, as a separate cryptocurrency, will take a long time to gain confidence from users.
If you are afraid it will supercede Bitcoin then buy some "Zerocoins" for your bitcoins. It's as simple as that. Cryptocurrency-to-cryptocurrency exchanges are extremely efficient, and you could hedge your position as you see fit, instead of forcing every Bitcoin user to adapt to your worst case scenario.
If this separate Zerocoin becomes more popular than Bitcoin, I'd be very happy! It would mean that it has greater value than Bitcoin to the people using it. Bitcoin is already amazing, improving it can only be positive. If you worry you will lose out financially on this, then, again, buy some "Zerocoins" for your Bitcoins.