This should work out fine provided that the systems at the new domain location are able to communicate with the systems on the original site.
SEP clients would need to be able to communicate with the SEPM on port 8014 and they would also need to be able to communicate with the GUPs on port 2967.
If you're using Windows XP as the GUP, it would be recommended to limit the amount of clients that are able to connect to update at one time because XP has a concurrent TCP connection limit of 10 & Windows 7 has a concurrent connection limit of 20.
So in summary, SEP communications do not have any dependancy on domain relationships so long as they are able to communicate with the other network.