Hi,
I suggest solution like this:
CS Launcher application will be developed that will monitor CS proces activity.
An player will download CS Launcher application from you site. Starting CS over this launcher will be required to acces your server. CS Launcher application will start CS, and during it's proces presence in memory will block "write operation" from any other process in CS proces memory range and install folder. Also your site will have an service providing two lists. First of known cheat applications process names so that louncher can download this list from your site and check that there are no processes with listed names in memory. If an process with listed name is found in memory the player will be informed that by your policy he can't use cheats while playing the game over your server. The second list will contain checksums of alowed CS builds so if an player has some 3rd party CS build with embeded cheat he will be informed that his build is not allowed on you server. This lists will be editable by you and your staff.
(Complete application code will be delivered to you)
Regards,
Ivan