There IS no "a" (indefinite article) in Greek. If the speaker means "a", he uses no article at all (you can't tell the difference in Greek between "rock" and "a rock"; they are the same).
In this passage, Christ doesn't say "the" -- he says "this very" - the word tauth -transliterated taute - you may recognize it from our word tautology. It means "the same". It's intensified with the demonstrative pronoun th , so it's not just "this rock" - it's "this very same rock right here". Don't see how he could be much more emphatic than that. It just isn't possible that he meant "a" rock.
Not at all if you "get" the metaphor.. If you do not get it, the metaphor can mean a number of things.. Thats usually why a metaphore IS used, to make a partivular point.. Not to forget he was talking about a meeting place made of many rocks.. while he was saying the very metaphor to THAT rock..
Is your Greek font missing iota subscipts? I would expect 'epi' to take the dative in that phrase.