On the other hand, a major responsibility of the FTC commissioners is to develop regulations for interstate commerce, a power that is solely granted to Congress. Allowing the President to disregard the rules Congress specified when delegating that power to the FTC is usurping Congress's regulatory powers and giving them to the President. At best you could argue that the laws that created the FTC commingle congressional and executive power in an untenable manner, and it will need to be restructured. But in the meanwhile, you still have to justify why congress limiting the executive's enforcement power is worse that the executive usurping congress's regulatory power. And more-so why it is necessary to do so in an injunction, when it contradicts long-standing precedent.
No, that cuts the other way. The only reason we allow the FTC to create regulations with the force of law is by pretending that regulations are just an expression of how the executive will exercise its delegated discretion in enforcing the law. That makes rulemaking a quintessential “executive power.”
Your argument amounts to the idea that, because Congress has done one wrong thing (allow the executive branch to make laws) it should be permitted to do a second wrong thing (allow the Article I “executive power” to be exercised independently of the President). That makes no sense. You can’t reward Congress for doing an unconstitutional thing by letting them do a second unconstitutional thing.