By Site Checker I assume you mean SiteAdvisor. That's optional so wont effect Security Center's behaviour.
VirusScan, however, is regarded as an essential component of any of the retail packages & has to be installed to avoid those alerts. Which means you would have to uninstall any other anti-virus that you may be using.
Only certain applications are available as separate packages and VirusScan or Firewall Plus are not.
Out of interest what other anti-virus are you using instead of VirusScan?
It is fine to use extra anti-spyware however. There are a few free ones we recommend listed here:
http://community.mcafee.com/showthread.php?t=136913