I see wild speculations are proliferating. so adding a basic data on Christianity in Japan extracted from Japanese wikipedia:
Persecuttion of Christinanity in Japan formally started in July 1587 with Kyushu edict forbidding missionary work, and requesting Daimyo conversion to Christianity to be approved by highest authority. The following problems in order of decreased severity were cited:
1) Problem with taxation of Christian subjects - they did not pay many taxes, mostly related to Buddhist shrines support.
2) Export of Japanese citizens as slaves, especially sex slaves
3) Religious violence (burning of shrines in particular)
The law was absolutely not enforced until San Filipe incident in 1596 though.
In 1596, the damaged Spanish galleon San Filipe has entered port Tosa, in Shikoku island. Crew was detained and cargo confiscated following Portugese claims of galleon being the scout of imminent Spanish invasion. Some reckless/bold statements from Spanish captain, and armed resistance by ill-disciplined, formerly piracy-associated Spanish crew has further convinced Japanese of Portugese allegations being correct. As a result, Franciscan order was expelled from Japan in 1597, and 26 missionaries (foreign and Japanese) were executed.
In 1602-1603, a lot of orders of Christian Church has arrived in Japan, notably Ausustines and Benedictians. Rivalry between Christian faction raised to unprecedented level, and new orders acted bolder and more aggressive compared to well-establisheds Jesuites.
In 1609-1610, Christian daimyo Arima was involved in serious corruption scandal related to compensation paid for incident resulting in 48 Japanese deaths in Macao (although incident itself was not related to christians). This incident significantly spoiled image of Christianity in eyes of Bakufu top leadership.
In 1612, additional area rule restricting Christians in Edo and Kyoto was enacted, citing a rising sectarian violence. Daimyo Arima was honorably executed after a prolonged legal actions.
In 1613 and 1614, following a flares of religious violence (associated most prominently with Siege of Osaka in 1614), country-wide bans on Chistianity with increasing scope and strictness were enacted. Jesuits were expelled in 1614, and open missionary activity in Japan has come to the halt.