If you want true MST, you would need to configure it on all devices within a layer 2 domain. MST does support backward compatibility to RSTP and CSTP if you wanted to leave some of your device in those modes.
The use case you suggest here is a little unusual. Typically you would setup MST on your layer 2/3 gateway devices so that you could have some VLANs terminate on one and some terminate on the other. You would align the root for each instance with the active gateway for a high availability protocol.
If you do not have commom VLANs between your data center and the rest of your LAN, you would probably be better off just separating the two with a layer three device, so they do not propagate spanning tree between them.