The architecture and design are very similar. The shape of the building and the interior of the main room resemble one greatly, plus the stained glass windows.i agree that it could be a worship place and i also agree that the temples were likely places of worship before monsters inhabited them but how is the temple of time identical to a church? there are no benches for people to sit. there is no podium for a speaker. the only podium in the place is for the spiritual stones to go. it really is just a big room with a place to put the stones and a back room where a sword lies. i dont see how it resembles a church in any way.
You're right, it is lacking some of the other things. But I don't think they'd necessarily need benches and a podium, as the Hylian religion doesn't seem to function that way. They don't go to church on Sunday or listen to preaching, etc.. They just all worship the Goddesses. The Temples (including the Temple of Time) could just be a place for someone to go and pray.
I don't believe the temples for Greek gods and goddesses had benches either.