Software Deployment

I created a msi to be downloaded from the web and to be installed on the computer through the web deploy method, but the security in this method where all the login information is stored in the MSI is diabolical. anybody with and ounce of brain will use this to download everything through the login.
i was wondering whether there is another way to do this securely?

i dont have to use wise completely, we can use the wise script editor, vb script, vb or anything else that makes sense to embed into the msi.

any help will be appreciated.

regards
yasi