I don't think it is possible, for commands to work you need to attach a local insim and use the MST? packet. Either way the only way to do it would be to have every client/player that joins your server to run your "clientSideInsimApp" and then that client would connect to your "serverSideInsimApp" which when the server wants to tell clients to load a set / run a script/command it would need to go to the correctly connected clientSideInsimApp and then use that insim connection to the local (players) LFS copy to invoke the command / script.
All in all, it is a long process, each player would need to run their clientSideInsimApp and it isn't very user friendly. I would urge against this idea because it seems a little intrusive, and players on your server systems would likely be lost when it tells them they can't join without first connecting the clientSideInsimApp.