Nintendo UK has clarified the Bayonetta 2 purchase options:

1) Bayonetta 2 solus

2) Bayonetta 1 + Bayonetta 2 (2 discs in one packaging)

3) The digital versions available in the Nintendo eShop in Europe will be sold separately

So yes, Europe will see the same deal as Japan. One thing seems certain: Bayonetta 1 will not be "free" after all.