This would be fairly easy to do, id be happy to give out a few ideas better suited but a fairly general way to do it would be to setup a PHP API
so in construct you would do a GET request to "www.MyWebsite.com/MinecraftInteraction?Action=RunCommand&Command=say hello there!"
The php script would then save the command to a mysql database
Your script would then (using skUtilities) do a get request to "http://www.MyWebsite.com/MinecraftInteraction?Action=GetLatestCommand" (This would output "say hello there!") and return it to your skript where you would simply run whatever you got back as an command or do error checking
This would make it possible for you to do commands directly or interact in other ways (You could use this for any data transfer between your server, website and construct 2 programs)
Now there are other ways to do this but no matter how you do this you need to include some sort of authentication to ensure only your application can send commands to the server!
Id be happy to talk more on this and possibly help you code it in if you are unfamiliar with php