This isn't about certification. This is about Apple making their products incompatible with products made by other manufacturers for no good reason. Microsoft certifying third party controllers is irrelevant; the controller works if it's made properly, regardless of whether or not Microsoft signs off on it.
You're still working under the assumption that iOS devices lock out third parry products that aren't MFI certified, which is not entirely accurate.
I can change an iOS device with a certainly *not* approved charger and cable just fine - the device doesn't stop it from working. What will occasionally happen is if the device you're attaching has been wired incorrectly or in a way that the iOS device does not expect. This isn't "locked out" so much as simply being made incompatible in the first place. For example, for USB chargers, there's a documented method to indicate higher current draw than the 500 mA mandated by the official USB-IF spec but if the device doesn't appear as a default USB device (and thus, the phone requests 500 mA) and doesn't have the right resistance across the pins (to indicate high power availability) then a message will pop up that suggests it's not supported. *Even in this case* the device can still function - the message is not necessarily blocking it from working, but serves as a potential caution.
This isn't always the case, for example, some adapters that try to pass plain line audio (which was supported on the 30 pin connector) to the lightning connector can result in an unsupported message since the pinout is not compatible, even with the lightning to 30 pin adapter.
As far as the headphones go, the connector is pretty simple with some basic control functions. There's no locking out of non-certified headsets and headphones that work via the extended 3.5mm jack.
For most devices, there's no "lockout" coming from the phone for things like headphones and chargers and so on.
This is also ignoring the fact that for antitrust to apply, the abuser has to be leveraging their *monopoly* position in one market to affect the situation in another market. The textbook example is Microsoft's monopoly position in operating systems at the time being used to force Netscape out of the browser market by using IE to squeeze them out, or using the Windows monopoly to force OEM PC vendors to only ship Windows-installed machines (and not a mix of Windows and OS/2) or face a rise in the OEM price of Windows licences.
In Apple's case, they're not in a monopoly position in smartphones, so there's no antitrust regulation to break - the market for headphones for cellular phones is not controlled by Apple. It might be a bit of a dick move on Apple's part, and highly retaliatory (note: it also wasn't used as a threat to drop the suit you notice, merely a result after the fact) but it's clearly not illegal.