How to Disable USB 3.0 and USB 2.0 while keeping USB 1.0/1.1 on Mac Mini?
All Intel-based USB host controllers use hardware-based DMA engine to execute linked list of TD (transaction descriptors) from main memory. This is/was true for all three of them, UHCI, EHCI, and latest xHCI. More, in recent Intel platforms the UHCI (which did handle full-speed and low-speed) is now abandoned. 

In intermediate USB architectures (Sandy Bridge, Ivy Bridge, series 7 chipsets) the only remaining controllers were EHCI and xHCI, which is still an eclectic mix. Funny, it looks like the FS/LS modes are handled via xHCI (USB3) controller if the EHCI controller determines that the attached device is LS or FS, and mark port ownership to "companion controller".

In recent USB architectures there is only one, xHCI type of controllers, which handles all modes (SS, HS, FS, and LS) uniformly via the same DMA access method.

So this is highly unlikely that you can avoid using xHCI USB 3.0 controller if you still want your USB keyboard and mouse.

You can try to use a regular HS hub to connect your keyboard and mouse. In this case the traffic will be controlled via EHCI HS controller (if this is C216 chipset), and xHCI can be disabled, if EHCI makes you feel more secure.