Yes, it can be used in that way. It sounds odd, though, worded that way. I don't know the entire context but "difficulties accompany" sounds stilted. I could imagine "have accompanied" or "will accompany" or "are accompanying".
It's just that "difficulties accompany" is too passive. Has the church been rebuilt? If so, the "difficulties accompanied". Will the church be rebuilt in the future? If so, "will accompany". If the church is currently being rebuilt, it should be "are accompanying".