Politics and religion can make for not just strange bedfellows but for trouble as well. It is perhaps the two-edged sword of Western expansion that brought Christianity along with it. It is not so much that it became safer to be a missionary in these places but that the door opened for it to happen. Of course, politically, the opening of that door was not often from the inside. The association of the arrival of missionaries with armies in the eyes and minds of the indigenous leaders is very understandable. For those who were touched by one or the other then their view is perhaps skewed against the other.
Jacques showed up in Madagascar with the French and faced opposition with local leaders for valid reasons, if one only looked at the political side. But he also made many missions and brought many to the Faith. This too can be a threat to political leaders. I do not know.
Whatever the reason he was martyred being shot after torture and having his body unceremoniously dumped into a river but not before expanding the Church.
Pray for all missionaries, that all will see the good in their work and give praise to the Father.
"God knows I love and if I still love and [the native soil and the beloved land of Auvergne]. And yet God gives me the grace to love more these uncultivated fields of Madagascar, where I can only catch a few souls for our Lord....The mission progresses, while the fruits are still in hope and in many places barely visible in others. But what does it matter, as long as we are good sowers, God will give growth in his own time."
-- From several Jesuit websites