That's just not true.
First, Bucharest is the largest and most diverse city in the country and is host to a significant population of Arab, Turk etc. students that live side by side with the locals just fine. The nearby Dobruja part of the country was under Islamic rule for the longest and has a sizable population of Muslims, mostly Tatars, that are integrated rather well.
The rare (very rare) clashes with Islamic stuff occur when some migrant with some Al Qaeda ties ends up locally, and I think there were like 2 cases of "online radicalization", zero terrorism.
There is no religious conflict between Muslims and Christians in Romania, and there won't be any in the future either, as long as they can avoid mass migration, which is the real cause of problems.
Also, while there are a lot of churches, not nearly all are Orthodox, many are "temples" from various Protestant cults or Catholic. And the Romanian population, while overwhelmingly culturally Orthodox in average, is touching those churches like 2 times/year at most. Religion is slowly dying across East Europe, but many groups have an interest to blow things out of proportion.