I was going through yahoo's dictionary, and for the most part the sentences are in casual form. This one isn't:

何時に学校は終わりますか?

Would it be rude if instead I asked:

何時に学校は終わるの？

My concern is whether saying 終わる　in polite form will make me sound awkward.

both are ok, just choose based on who you are talking to.

Although frequent use of の as a question marker sounds effeminate.

There's nothing special about the verb 終わる that dictates that its politeness level should be different from any other verb, but the sentence sounds slightly unnatural.

学校は何時に終わりますか?
sounds better in my head.