Best way to handle situations where you need to maintain separate balances

Okay so here goes, assuming I build say a faucet and a mining pool, what would be the best way to maintain separate balances to prevent any crossover issues between the scripts and them touching coins they shouldn't.

I already know I could create an overlay that tracks the balances separately similar to how things work that have to maintain individual user balances, but I am wondering what other options there are besides running multiple copies of the daemon and duplicating the block chain data and what is the best way to handle this. I have looked into importprivatekey and that doesn't even look remotely feasible since it will cause the wallet to be unavailable for a period of time due to the rescan not to mention the load overhead that would occur anytime access was needed to a wallet that wasn't currently active.

I have been thinking on this for quite some time, as well as doing a considerable amount of research trying to figure out the very best solution for this, and now I am curious to see what others have to say about this scenario, seeing as the more I plan out my project(s) the more I am starting to need additional wallets/unique balances.