While the committee is targeting all phone makers operating in Europe, Apple is one of the only companies that doesn't already supply users with a Micro-USB connector. For the most part, phone makers in Europe broadly adopted Micro-USB cable chargers after the European Commission chose the interface as the region's official standard in 2010.
How this law is written will dictate whether Apple will be compelled to respond. It could be that Apple ends up paying a fine each year for non-compliance. There's also the possibility the EU plans to aggressively enforce the law by seeking injunctions against products that do not comply.
I see a couple of interesting scenarios potentially playing out. The most unlikely of which involves Apple yielding to the EU's wishes. The more likely scenario I could see happening is Apple licensing the lighting connector (or more likely just release the spec) to other phone makers, and presenting it as a new standard. If faced with the choice, it will be interesting to see what Apple values more: a proprietary connector, or having control over what connector it uses in it's European phones. The law also has the potential to impact Apple's phones in other countries too.
If the opportunity presented itself, I'd fully expect Apple finds a way to resolve the situation in some way that maintains the status quo. I think Apple likes the Lightning connector, and they'd like to keep it proprietary. As you may know Apple does have piles of overseas cash. A yearly, or per product fine may be the solution.