I`m not Christian, and can`t say I enjoy those who come around and attempt to convert people (and I doubt it will win you any friends in Japan...)
But I can`t say I am against Christianity or practicing it - anything that encourages someone to be a better person is nothing to be
against, in my opinion.
There are a number of smaller churches in Japan, and I am guessing that with the small number of Christians they have tightly knit communities. I am absolutely sure that you would have no problem finding a church to help, even if not in a mission capacity. Although I imagine it will be hard to be picky when it comes to denomination - barring a few exceptions I have only seen churches listing themselves as "Christian", with no denominational attachment. There is a small church somewhat near me, and they are always advertising gatherings. I have also spotted the church name reserving gathering places, etc, for parties and get-togethers. They seem to be very active.
It LOOKS like there are a number of large churches in every town, but they`re almost all fake.
Part of "Dream Wedding" complexes.