I'm confirming it with my Win32 1.0.0.338 beta 2 build:

alter table "Activities" add constraint fk_activities foreign key
("Company") references "Agents" ("Id");
commit;

then

alter index rdb$foreign64 inactive;

=>

This operation is not defined for system tables.
unsuccessful metadata update.
MODIFY RDB$INDICESS failed.
action cancelled by trigger (3) to preserve data integrity.
Cannot deactivate primary index.

Dmitry