Yes the science was bad, but what else is new. I could start listing episodes that had completely absurd fallacies about science. The Tenth Planet, The Twin Dilemma, The Impossible Planet/The Satan Pit, Journey's End, The Three Doctors,The Armageddon Factor, Underworld, off the top of my head,… But this is a story about an alien that turns into another person every time he dies and flies around in a police box that's infinitely large on the inside. Perhaps this egg was more like a womb and it consumed mass/energy from outside sources.
It's actually a lot more of an RTD thing to do...a ridiculous, grandiose idea as a vehicle to show some personal character moments.
I found this episode to be ridiculously intense - I wasn't sure what to think about it for most of the time, but I actually really loved the ending. There were a lot of Tom Baker channeling moments. Regardless of the science, the scene on the beach was superb. I was asking myself for a while where the heart of the episode is, and I felt like I got it in spades.
To the fight at the end: I know that what the Doctor did was technically right, however, this is not way he ever has done things. Clara had every reason to be upset - he withheld information, and just took off, leaving her to make a HUGE decision, possibly die, and not know if he was coming back. He went too far. She's starting to realize that this doctor is very different from the one she started with. Also, she had a point that he IS invested in earth, he can't just decide to remove himself on a whim when he feels like it.
As for the supposed pro-life message...Neither me nor my fiance even had a hint of a thought about that until I got on the internet. I can see where people can get that idea, but I think it's a bit of a stretch to think that the author is trying to convince people of anything. It reminded me a lot of "The Beast Below" and a myriad of stories int he classic series where the Doctor tried to convince humanity not to kill something they didn't understand out of fear, and instead learn from it. I guess it wouldn't be the first time writers inserted their personal views in, though...there was a lot of Eastern religion influences in the 70's and 80s, and Robert Holmes purposely made "The Two Doctors" a platform for vegetarianism, though I felt like it backfired and made me want to eat meat ;)