That's an interesting suggestion that originally animals and man spoke the same language. Just the other day I was wondering about the talking serpent in the Eden account. The account is really saying that all snakes could talk back then, not that one snake was possessed by Satan, as Witnesses will say. So I was wondering to myself, "Why could snakes talk then and not now? Didn't the Jews have any explanation for that in one of their stories?" It seemed like the sort of loose thread that would warrant some kind of explanation, and the Eden account doesn't say that the snake was stripped of its speaking ability.
So perhaps this Babel account originally more clearly stated that the animals could still communicate with men. However, as it stands, the account says "all the earth", not "all of the earth's creatures" or some similar phrase that could refer to non-human animals. I just take it to be a poetic phrase referring to all of human society.
It's actually an odd choice of words, since all humans were living in one little area at this point, post-Flood. If this story is misplaced, though, and belongs before the Flood, it makes more sense. In fact, it makes more sense anywhere else than where it is, such as well after the Flood when there would have been more people for such a project. As you indicated, this part of the Bible is a mishmash of old stories. It's likely that the Babel story was not originally part of some timeline or continuity that included the Flood story, and that's why it's not very compatible with it.
As to what it was that God (or the gods) were afraid of, it was probably just the tower itself, since if it was built up to the firmament, then perhaps it could be used as a siege tower in an assault on heaven. Later religious leaders, in a time where God was (or the gods were) more powerful, might have found this idea of an assault on heaven challenging to the majesty of the gods, and so they distanced themselves from the original premise by having the men say, "We will make a celebrated name for ourselves." The gods then say in response, "If man can do this, then he could do anything, and it's an affront to the gods for man to think so much of himself", thus explaining the language confusion as a punishment for hubris rather than a defensive maneuver in a war between earth-dwellers and heaven-dwellers.
As to who the gods would be, we know that early Jewish culture is in fact Canaanite culture, and initially they shared the same polytheistic beliefs. So the gods would likely be the 70 sons of El (or some later derivative of this belief), as discussed in various places on this forum. See Leolaia's posts here: http://www.jehovahs-witness.net/watchtower/bible/165791/1/YHWH-a-minor-pagan-god-Ugaritic-Texts-and-the-Sons-of-El