Anyhow, they broke it so they should fix it at their cost (in my opinion) - quite a few service manuals i have read say that you should loosen the bleed nipple before attempting to push the pistons back to prevent this occouring.
When I push or wind back caliper pistons, I always loosen the bleed nipple and drain off the fluid from the caliper. Several reasons:
- The reservoir may have been topped-up as the pads wore; so would overflow if the pistons were simply pushed back
- Fluid in the caliper is dirty and may contain most of the moisture (being the lowest point in the system) - why push that back up into other parts?
- If there is air trapped in the caliper, this is a quick way to bleed it out
- ABS modulator valves CAN jam - especially on Hondas that have a unique two-part ABS system (I learned that the hard way many years ago)
- Master cylinder seals can reverse, as described
Whatever it is, it is now the problem of the garage. They should first try pressure-bleeding - where the reservoir is pressurised to push clean new fluid through the system (no pumping the pedal...) If that doesn't work, they should replace the master cylinder and may even have to replace the ABS modulator if they're unlucky.