>The real issue is that we never want people at Active Directory Site X to be able to run our VFP compiled EXE unless they are using TS. So, I'm thinking we could check for the environment variable called LOGONSERVER as we just have one replicated AD Domain Controller at that site and if they are logged on to that server it should not let them use our EXE. Now if TS shows that same LOGONSERVER then maybe we'll have to allow them to run it if they are in TS. Is that confusing?

Yes it's. :)
Maybe you can combine check for TS with some AD attribute of a user that specifies SIte X? See Re: How to get the full username(displayname) from the AD Message #984716.