I don't see this happening, but even if it happens, it would risk escalating the issue. Germany has much weight in the EU and as stated the EU is already investigating Apple Pay. If Apple pisses-off Germany it might find itself at the wrong end of EU regulations: then the choice is to comply or forfeit a market of 500M people...I don’t agree here. For Apple, Germany is currently a smaller market than say Australia, they can totally afford to take the hit by pulling Apple Pay put of the German market.
To me it's clear that the EU frowns at anti-competitive practices and considers Apple's locking of the NFC capabilities on their devices anti-competitive: the question is only whether the current anti-competitive legislation is enough for them to act, or the EU needs something new. Likely it's the latter and Apple pissing-off Germany could easily be what triggers it to happen.