In a nutshell. [url=http://io9.com/black-widow-this-is-why-we-can-t-have-nice-things-1702333037]This article[/url] is pretty fantastic, and basically sums up all the issues with Widow. I can't find a single thing in it I disagree with, and it made me notice a lot of stuff I hadn't while my brain was just going 'wheeeeee, explosions!' at the cinema.is that what the problem that everyone is having with the way she was/ is written?
Bottom line, Widow's done fairly well in A:AoU, but there are still deep, deep problems.
As for the issue you discuss, one of the comic writers' who is most directly responsible for the modern version of Widow was talking in [url=http://io9.com/how-to-make-black-widow-truly-awesome-according-to-ric-1703159410]this also excellent article[/url] and summed up that SPOILER the issue isn't that she wants children but can't have them; basically she's not really interested in having them, so she's not angry about that. She's angry that her choice was taken away; that she was made subservient to others. It's a subtle difference, but it's really really significant. So yeah, problems as far as she's been written so far. The nice thing about the MCU though is that it's basically a work in progress, and as the Marvel short 'Hail To the King' showed, they're happy to retcon stuff that fans don't like.
Even though I bloody loved The Mandarin in 'Iron Man 3'.
As for Tony Stark wanting to give the Avengers a chance to just live normal lives and go home through his preemtive planning, well. [url=http://tvtropes.org/pmwiki/pmwiki.php/Main/VillainsActHeroesReact]Villains act, heroes react.[/url] It's one of the central tenets of almost all superhero stories, so much so that there have been all kinds of interesting comics which look at what happens when the heroes start acting instead of reacting.
My favourite is probably [url=http://tvtropes.org/pmwiki/pmwiki.php/ComicBook/TheAuthority]The Authority[/url] by Warren Ellis, which poses the question 'What would happen if the Avengers/ Justice League basically decided to stop fighting supervillains and start taking on real-life villains like dictators and other undesirables?'
They become a fascist world-police of terrifying efficiency. The thoughtlessly grotesque Mark Millar version from later on is complete crap with Millar's signature 'and now for a pointless rape scene because that's edgy' style (obviously) on account of Mark Millar is a knuckledragging, woman-hating, no-nothing f**kwit whose work it is literally impossible to hate too much, but the Ellis run is superb. All through the comics, the Authority are wracked with doubts and issues about right and wrong, and in every way it reads very much like a typical superhero team narrative... Apart from the fact they're imposing their political systems on a world to which they allow no say. Ellis explicitly said that he wrote them as a supervillain team for this exact reason.
Hopefully, this is where 'Civil War' will go: with Stark convinced that security is more valuable than freedom, and Cap convinced that freedom is more valuable than security. Actually acknowledging that those two things exist on a continuum and that you can't have both at the same time. It would make for some genuinely excellent moral/ethical discussions about real things that matter amidst all the explosion.