So I may be able to answer myself finally. After some more research I found that there may be some confusion in how the systems are named. What is meant by a brake-by-wire system is usually a braking pedal that is mechanically decoupled from the rest of the braking system. This is different from what I actually need to do, because I do not need any pedal action at all, I just need to control the brakes electronically even on say a "non-brake-by-wire" car.
This is the system with a decoupled braking pedal. This site mentions two types of systems - electro-hydraulic and electro-mechanical. You can research them there. These systems seem not to be standard on today's car at all, there were few models by Mercedes and Toyota in the past 10 years or so some of which had to go through recall because the system was unreliable.
Braking by electronics (ESC/ESP etc.)
Obviously ESC/ESP can brake individual wheels by itself which is a kind of "brake-by-wire" to me but the industry does not call it so. This "autonomous braking" seems to be done by Hydraulic Control Unit (HCU, sometimes HECU) which is usually common for both ABS and ESC. This unit sits behind the master braking cylinder and has 2 fluid inputs but 4 fluid outputs (one for each of 4 wheels). For normal braking the unit just lets the braking fluid pass through without any intervention. The unit has an electric pump attached to it and if ESC wants to brake a wheel it seems to choose one of the 4 outputs and pressures it by itself (without the pressure input from master cylinder).
The bad thing here for me seems to be that the HCU is a black box in terms of software - it gets inputs from various sensors (wheel speed, yaw rate etc.) and decides by itself which wheel to brake. So in order to be able to initiate a braking action externally one would need to either send input signals that would result in all 4 wheels braking (need to reverse engineer the unit first and I also doubt such signal combination even exists) or hack the electronics to in lower level to pressure all 4 brakes in the same time.
Another solution for me may be to leave the HCU alone and make the system pressurized somehow else. I found there is a part called "electric vacuum (booster) pump", although I have not done deeper research on it yet. Any hits are welcome! :)
It indeed looks like there are ABS/ESC HCU units today that can accept external signals to initiate the braking. These units are used in cars with Autonomous Emergency Braking systems. The TRW EBC460 is said to have AEB feature and seems to have a CAN bus so I suspect it may be able to accept certain can bus messages that initiate the braking.
AFAIK most hybrid vehicles provide means of doing brake-by-wire in order to allow for "regenerative braking". They do not 100% mechanically decouple the brake pedal from the brake system itself (there remains a certain mechanical connection for emergency case) but allow for programmatic braking control for the most braking scenarios (probably all except panical emergency braking). This is why hybrid vehicles are very popular for autonomous car research (Google's Toyota Prius etc.) because they in general are very easy to convert to 100% programmatic control (steering, accelerating, braking). The brake-by-wire really is a "killer feature" of hybrids and 100% electric vehicles for autonomous car research purposes.