Churches here have a highly visible protruding cross (which is an Idol) on the roof and at many places all over the structure, does that mean the church itself becomes an Idol, i.e a large Idol, also passerby Christians make gestures of worship showing a gesture of kissing the church in air, paying reverence and devotion to the church, so does such a church as a whole be seen as an Idol?
Rambam AZ 8:4
So if the building is designed to be an idol and is worshiped then it is forbidden. But don't confuse worshiping an idol attached to a building with worshiping a building itself. You'd have to evaluate every building individually.
As has been discussed previously here -- no.
Even something like a plain cross (let's assume no one is on it) is often treated in Halacha as a symbol of the religion, but not an "idol" per se.
A building constructed specifically to house/protect idols would be considered "something used for idolatry" and therefore prohibited from use. Not because the building is an idol, but because we go so far as to prohibit using things that service idols. Hence, if a building was built from the ground up as -- let's say a Hindu temple or a Greek Orthodox church [we'll assume for now that the statues in each qualify as 'idols'] -- then a Jew could not buy that building and use it as an office, house, synagogue, or anything else. However, a responsum from over a hundred years ago (there's a Rabbi Frand tape about it) allowed Jews to buy a Welsh-Scottish Methodist church and convert it into a synagogue, as there are no "idols" inside.
Let me stress once again -- if something is an idol, that means you are prohibited from deriving any benefit from it. It does not give you any right to damage any person or property.