The Madoka characters deal with fighting monsters just as well as in any other Mahou Shoujo story. The thing that breaks the characters is the revelation of their purpose in the Incubator's machinations, as well as the nature of their souls and bodies after contracting.
The cute mascots are always addressed and explained. Kyuubey's motivations being darker than others does not make him a deconstruction of the archetype, it merely makes him different.
I don't remember any of their secrets getting out or being in danger of getting out, are you sure we watched the same show? Madoka simply ignores the possibility of their identities getting revealed because it's not a detail worth focusing on in its relatively short runtime. I can't imagine who you are talking about in any of your examples.
Again, intercast conflict should have nothing to do with any definition of "deconstruction." The characters coming into violent and deadly conflict with each other is absolutely no more "realistic" or logical than the more child-friendly resolutions in typical Mahou Shoujo.
And I think I've already adressed why characters dying isn't a deconstruction of genre conventions. At best you can say it's a subversion but subversions are not inherently valuable. Mahou Shoujo is not even remotely close to the only genre to regularly pit characters in dangerous situations but never cause any deaths. Death toll has nothing to do with genre and everything to do with both the demographics and the potential purpose those deaths can serve.
Madoka is one of my favourite anime so don't think I'm here to shit on it, but this deconstruction meme should have died a long time ago and I could have sworn it had. If anything Madoka should be seen as a reconstruction of the Mahou Shoujo genre, since it applies a lot of the darkest possibilities to the narrative devices and typical plot beats, yet in the end ultimately reaffirms that the foundational backbone of Mahou Shoujo is still correct.