I like a number of things (like the black ooze being derrived from the Alien, which I've often theorised), but, yeah, the Queen is too obviously a part of the default reproductive system to be dismissed like that, in my view. Especially since she's clearly optimised, symmetrical, etcetera. That's far from what a cancerous-style genetic mutant would look like.
I still say there's room for a future story to depict egg-transformation as an emergency method to obtain,
specifically, Queen-hosting facehuggers. That makes everything fit together.
Amanda suffocating to death on LV-426 would have been... Hmm... I don't know. Like, there's some interesting poetic irony in there, but it would have also felt like it cheapened Ellen's discovery about her in the film, because we'd know, in hindsight, that she's heading off to where her remains would be and just has no idea, which would have weird vibes. Depends how it's executed.
I mean, I personally don't embrace the EU version of Amanda as canonical, regardless. But in a comic, could have been an interesting hypothetical, depending on the eventual execution.
A rogue biologist declaring it's ridiculous to try and weaponise the Alien, I would disagree with. So long as the controlled laboratory conditions are there (and protocols are followed), without cutting corners, the Alien should be a lot easier to manage than, say, ebola, anthrax and all the other crazy plagues which have been kept in isolation in special facilities for decades. Especially if you do it on something like an orbital platform. They wouldn't even need a live creature. '
Resurrection' depicted a fairly incompetent operation and not how it would realistically be handled.
Heck, by that point in time, it would probably just be run by droids, anyhow. Zero human employees. Entire sections able to be flooded with radiation, ultrasonic countermeasures and a lot more. We only ever see very superficial, cartoonish depictions of how handling the Alien (or, at least, the DNA) would really be done.
Now, warning against an organisation trying to get ahold of them, which doesn't exactly have a great track record in safety? The 'wrong' people? Now you're talking!

There are even some real historical examples of stuff like that to reinforce their point.