Sorry, Luke. You know how it is around here . . .
I'll say....
So, if Luke's an anarchist, what am I? I'm trying to think of a stronger term for anarchist and I'm failing, and I haven't even begun to try to figure out how to describe Amir...
Anyway, seriously speaking I wouldn't worry too much about the anti-address-reuse patch right now. It's a very good temporary nudge in the right direction - I fully support Luke for implementing it - but it's against miner incentives to do it by leaving tx fees on the table. In the long run I'd be really surprised if the idea becomes all that common, and if it does, adding anti-anti-addr-reuse to MasterCoin is always possible by community agreement. If it's not much work to implement, go for it, but I've reconsidered a bit on this topic and right now my gut feeling is don't worry too much.
What you do need to do is make sure that MasterCoin tx's work fine no matter how many blocks separate them; I seem to recall something about six blocks at one point in the discussion? The number of consecutive blocks by any one miner is unbounded after all.
edit: BTW this applies to ideas about merge-mined chains too: you can always implement that later if they're needed. Focus on getting the core functionality and community that you think makes MasterCoin worthwhile up and running now rather than getting distracted. You gotta remember that MasterCoin transactions will tend to be more valuable per transaction than Bitcoin ones, so it won't be your users that are outbid first in the transaction fee auction.