Chris,
Two scenarios:
1. Do not create the STP domain at all on the MLAG peers. This is probably only a good idea if the VLANs going to the other devices only exist on ports 28 and 29 in the old topology. In this scenario BPDUs would be forwarded (actually flooded) from one 3rd party device across the ISC to the other 3rd party device. The two switches would basically act like a wire segment for the STP domain. However if other ports are added to these VLANs, BPDUs will be flooded to them as well. This may be undesirable. The main concern with this option is that the connection between the two 3rd party switches could be blocked by STP, forcing all traffic between those switches to be forwarded up to the MLAG peers and across the ISC. You may not want that traffic constantly going across the ISC. It doesn't sound like you have control over the configuration on these switches so this is something you might have to test/investigate.
2. Add the ISC to the MSTP configuration as you have mentioned above. The concern here is that the ISC could potentially be blocked by STP. Making one of the MLAG peers the root bridge would be one way to help ensure the ISC is never blocked. I don't know how feasible this is because I don't understand the full STP topology. This option could also introduce the same problem with traffic being constantly forwarded across ISC due to the link between 3rd party devices being blocked.
With either option, it may be best to have control/insight into both network segments so you can tweak STP cost and priorities so that you can have it behave exactly as desired.