Looks like the controversy has abated. Jaanus has posted an explanation of his earlier comments, making clear that others within Skype had indeed had experiences similar to mine in setting up vSkype. Stuart from Santa Cruz, in his followup, states that vSkype has been downloaded 200k times already, which is interesting. I'm relieved I didn't start some sort of panic based solely on my own confusion.
Perhaps the vSkype startup process should actually ask you to identify individual contacts you want to add, rather than asking you to de-select those you want to exclude. The former approach probably leads to maximum proliferation of the service, but as in this case, may lead to misunderstandings.
One other thing I'm curious to understand. I have set my Skype client NOT to start when I boot up the machine, but to wait for an explicit startup command. This has always worked in the past - until I installed vSkype. Now, even though the client is still set not to launch automatically (tools/options/advanced/startup/