There is confusion in your question. Which of the follow are you worried about exactly?

1) potential interference between different altcoin wallets?

My comment: why would there be any interference? Many people install several coin wallets on the same machine and they get along quite well.

2) interference across wallets belonging to different users?

My comment: If you're worried about this, you should rethink the way you implement multi-user wallet management. Check out my other response on this topic: https://bitcointalk.org/index.php?topic=406742.msg4441020#msg4441020  Hint: you only run one single wallet instance for the whole website.