It is possible to deactivate a partnership with the 12.7 (and newer) REST API.
In the FedSPPartnership or FedIdPPartnership object, there will be a "status" attribute.
The values supported are: Active, Inactive, and Defined.
Active: Partnership is active and in use.
Inactive: Partnership is inactive and will not be used.
Defined: Partnership was recently created/modified and is not active or in use.
Note: There was a defect in 12.7.0 that did not allow the modification of Federation Partnership objects when the Policy Store was upgraded directly to 12.7 from a previous version. This was fixed in 12.7.1 and later.