For the most part I agree with you about monsters being possibly too much for Traveller, but maybe it is also a function of age among the players. I was only 15 when the game came out and I was playing Metamorphosis Alpha and D&D at the time. I never had any of those "oh, c'mon" moments in the early days of my Traveller campaign no matter what I threw out there.
Over the years, though, it seems like as I matured (or at least aged) my campaign seemed to get a little stodgy, or at least I had to work harder to keep less plausible things in it rather than turn the whole thing into something harder and duller. But I have been (lately) kind of missing the old days when my imagination could run wild without having to rationalize and justify everything and be more free. Like when I was a kid.
As a result MTU now has a whole half a sector on the other side a of vast rift from the rest of the campaign that is full of all sorts of wild and wooly alien worlds, and lurking in the nebulae are some fearsome space beasties rumored to eat ships passing through. This is my "Alice In Wonderland" universe where it is very much more space opera (though I still have plenty of that in regular game) with lots of Barsoom/Tschai types of things in it and since the entire theme is more out-there, it makes it more 'safe' for me to introduce any weird idea I swipe from pulp scifi, anime, or comes from too much coffee hagen-dazs and painkillers.
SO I think you could have space whales in Traveller, it's just that the rest of the campaign has to support that sort of thing somehow, and rationailizing them with even psuedoscience seems to fail the suspension of disbelief test. At least for me. I'd rather just say "there be whales" and leave it at that, and since there are also things like talking otter slavers that eat human crews and electric eels for snacks to contend with, the space whales are easier to swallow. The whole theme of the game supports them.