Yes, you can run a script on the server on any map. If you want it to happen automatically you might need to get the server to add a line to their server.cfg file to execute it, or create a mapspawn.nut file with some instructions, but if a map has its own mapspawn.nut file it might override. And of course SourceMod can run VScripts.
What is it you wanted to do using VScript that you can't do using SourceMod?