No, he's worried about malicious code embedded into alt-coin clients which would have access to the user on the server where they are located.
IMO this is quite a tertiary worry. Of much more importance is that of attackers gaining root access to the machine where the wallets are located, executing a few commands and emptying all the coins.
That has been the most common attack vector in bitcoin related businesses. Better to design something to secure the coins where you assume the attacker already has root access.
Cheers, Paul.
I am working with him on this, actually what we want is just a list of security tips from the community so that we can ensure maximum level of it nad what he said.
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.
No that's not what he meant. We are worried about malicious code in the wallet(I can't go into much details right now)