Comparing the Behemoth's weapon to that of the Tiamat/Kraken is like comparing apples and oranges -- a perfectly sensible thing to do, as long as you're not just trying to find out what apples taste like.
The Behemoth is a big gun used to destroy certain planets -- tectonically unstable ones, according to the WC3 novel. It'd have a devestating affect on others, but not the total destruction seen at Loki. Although I would agree with the asertion that Confed may still have Behemoth class ships, I would argue that they are not particularly useful for several reasons, from a tactical standpoint, namely...
The Behemoth is a *large* target -- over 100 times as long as the Sivar Dreadnought (which mounts a technology Confed *has* mastered). Even with full shields and weapons -- and there's no reason to think these go "down" when it fires... that didn't happen to Concordia or the Sivar or any other large-gunned ship -- Behemoth is still a huge target to protect.
There's the issue of effectiveness. Who wants to destroy a whole planet? Confed has spent the lives of billions of marines to *capture* enemy worlds -- the Behemoth would *destroy* them, rendering useless the potential real estate.
Proportion -- Behemoth makes the biggest bang... but *not* the biggest bang for your buck. The Atomic Proton Accelerator Gun wipes entire colonies off the map (and leaves planets habitable!) and, when mounted on the Sivar, was 100 times smaller than Behemoth.
And then there's the fact that there are no planets to blow up -- why the heck would Confed build *more* Behemoths when facing the Nephilim? We are fighting a limited, defensive war... we have *no* way to hit their home territory at present. And I don't think that, even if Confed and Kilrathi worlds were captured, that anyone would approve wiping them off the face of the galaxy.
There's also the issue of cost and reload times. The Behemoth is *expensive* -- and it takes a new load of fuel to refire it. A *lot* of fuel -- an entire convoy worth. It's also too slow to aim at moving targets -- while its weapon would be effective against ships, none would stand in its maw long enough to be hit.